| 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. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 5. |
- Li, Sirui, et al.
(författare)
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Glioma grading, molecular feature classification, and microstructural characterization using MR diffusional variance decomposition (DIVIDE) imaging
- 2021
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Ingår i: European Radiology. - : Springer Science and Business Media LLC. - 0938-7994 .- 1432-1084. ; 31:11, s. 8197-8207
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To evaluate the potential of diffusional variance decomposition (DIVIDE) for grading, molecular feature classification, and microstructural characterization of gliomas. Materials and methods: Participants with suspected gliomas underwent DIVIDE imaging, yielding parameter maps of fractional anisotropy (FA), mean diffusivity (MD), anisotropic mean kurtosis (MKA), isotropic mean kurtosis (MKI), total mean kurtosis (MKT), MKA/MKT, and microscopic fractional anisotropy (μFA). Tumor type and grade, isocitrate dehydrogenase (IDH) 1/2 mutant status, and the Ki-67 labeling index (Ki-67 LI) were determined after surgery. Statistical analysis included 33 high-grade gliomas (HGG) and 17 low-grade gliomas (LGG). Tumor diffusion metrics were compared between HGG and LGG, among grades, and between wild and mutated IDH types using appropriate tests according to normality assessment results. Receiver operating characteristic and Spearman correlation analysis were also used for statistical evaluations. Results: FA, MD, MKA, MKI, MKT, μFA, and MKA/MKT differed between HGG and LGG (FA: p = 0.047; MD: p = 0.037, others p < 0.001), and among glioma grade II, III, and IV (FA: p = 0.048; MD: p = 0.038, others p < 0.001). All diffusion metrics differed between wild-type and mutated IDH tumors (MKI: p = 0.003; others: p < 0.001). The metrics that best discriminated between HGG and LGGs and between wild-type and mutated IDH tumors were MKT and FA respectively (area under the curve 0.866 and 0.881). All diffusion metrics except FA showed significant correlation with Ki-67 LI, and MKI had the highest correlation coefficient (rs = 0.618). Conclusion: DIVIDE is a promising technique for glioma characterization and diagnosis. Key Points: • DIVIDE metrics MKIis related to cell density heterogeneity while MKAand μFA are related to cell eccentricity. • DIVIDE metrics can effectively differentiate LGG from HGG and IDH mutation from wild-type tumor, and showed significant correlation with the Ki-67 labeling index. • MKIwas larger than MKAwhich indicates predominant cell density heterogeneity in gliomas. • MKAand MKIincreased with grade or degree of malignancy, however with a relatively larger increase in the cell eccentricity metric MKAin relation to the cell density heterogeneity metric MKI.
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| 6. |
- Liu, Wei, et al.
(författare)
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Pickering multiphase materials using plant-based cellulosic micro/nanoparticles
- 2024
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Ingår i: Aggregate. - 2692-4560.
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Forskningsöversikt (refereegranskat)abstract
- Pickering multiphase systems stabilized by solid particles have recently attracted increasing attention due to their excellent stability. Among various solid stabilizers, natural and renewable cellulosic micro/nanoparticles that are derived from agricultural and forestry sources have become promising candidates for Pickering stabilization due to their unique morphological features and tunable surface properties. In this review, recent progress on forming and stabilizing Pickering multiphase systems using cellulosic colloidal particles is summarized, including the physicochemical factors affecting their assembly at the interfaces and the preparation methods suitable for producing Pickering emulsions. In addition, relevant application prospects of corresponding Pickering multiphase materials are outlined. Finally, current challenges and future perspectives of such renewable Pickering multiphase systems are presented. This review aims to encourage the utilization of cellulosic micro/nanoparticles as key components in the development of Pickering systems, leading to enhanced performance and unique functionalities. image
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| 7. |
- Sun, Wenbo, et al.
(författare)
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Quantifying H&E staining results, grading and predicting IDH mutation status of gliomas using hybrid multi-dimensional MRI
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Ingår i: Magnetic Resonance Materials in Physics, Biology and Medicine. - 0968-5243.
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To assess the performance of hybrid multi-dimensional magnetic resonance imaging (HM-MRI) in quantifying hematoxylin and eosin (H&E) staining results, grading and predicting isocitrate dehydrogenase (IDH) mutation status of gliomas. Materials and methods: Included were 71 glioma patients (mean age, 50.17 ± 13.38 years; 35 men). HM-MRI images were collected at five different echo times (80–200 ms) with seven b-values (0–3000 s/mm2). A modified three-compartment model with very-slow, slow and fast diffusion components was applied to calculate HM-MRI metrics, including fractions, diffusion coefficients and T2 values of each component. Pearson correlation analysis was performed between HM-MRI derived fractions and H&E staining derived percentages. HM-MRI metrics were compared between high-grade and low-grade gliomas, and between IDH-wild and IDH-mutant gliomas. Using receiver operational characteristic (ROC) analysis, the diagnostic performance of HM-MRI in grading and genotyping was compared with mono-exponential models. Results: HM-MRI metrics FDvery-slow and FDslow demonstrated a significant correlation with the H&E staining results (p <.05). Besides, FDvery-slow showed the highest area under ROC curve (AUC = 0.854) for grading, while Dslow showed the highest AUC (0.845) for genotyping. Furthermore, a combination of HM-MRI metrics FDvery-slow and T2Dslow improved the diagnostic performance for grading (AUC = 0.876). Discussion: HM-MRI can aid in non-invasive diagnosis of gliomas.
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| 8. |
- Xu, Huan, et al.
(författare)
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Osteoconductive and Antibacterial Poly(lactic acid) Fibrous Membranes Impregnated with Biobased Nanocarbons for Biodegradable Bone Regenerative Scaffolds
- 2021
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Ingår i: Industrial & Engineering Chemistry Research. - : American Chemical Society (ACS). - 0888-5885 .- 1520-5045. ; 60:32, s. 12021-12031
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Tidskriftsartikel (refereegranskat)abstract
- Carbonaceous nanostructures featuring unique structural characteristics and high cytocompatibility offer a wealth of possibilities to impart enhancements of mechanical properties and biological activities for osteogenic tissue scaffolds. Here, we unveil the fabrication of osteoconductive and antibacterial porous poly(lactic acid) (PLA) membranes by direct electrospinning of microfibers impregnated with coffee-ground-derived quantum dots (QDs). It enabled a straightforward pathway to regulate the diameter and its distribution for the electrospun PLA microfibers, as well as the improved hydrophilicity. The QDs exhibited high affinity to the PLA matrix, permitting remarkable promotion of tensile strength and elastic modulus for the QD-modified PLA membranes while maintaining comparable extensibility. More importantly, osteoblast adhesion and stretching on the electrospun membranes were significantly enhanced with the existence of QDs, as exemplified by the nearly 1.8-fold increase in cell viability cultured onto the composite membrane loaded with 1.5% QDs compared to that of pure PLA. This was accompanied by rapid biomimetic mineralization and uniform apatite formation in an osteofriendly manner. Unexpectedly, immediate and broad-spectrum antibacterial performance was achieved for the composite membranes, likely arising from the synergistic effects of QD-imparted membrane stress and oxidative stress. The unusual combination of mechanical, biomineralization, biological, and antibacterial performances makes the biodegradable membrane scaffolds promising for guided bone/tissue regeneration therapy.
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| 9. |
- Zhang, Huan, et al.
(författare)
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Synergistic effects of warming and eutrophication alert zooplankton predator–prey interactions along the benthic–pelagic interface
- 2021
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 27:22, s. 5907-5919
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Tidskriftsartikel (refereegranskat)abstract
- Contemporary evidence suggests that climate change and other co-occurring large-scale environmental changes, such as eutrophication, will have a considerable impact on aquatic communities. However, the interactions of these environmental changes on trophic interactions among zooplankton remain largely unknown. Here we present results of a mesocosm experiment examining how a couple of zooplankton predator and prey taxa with different life-history strategies respond to the combined effect of an increase in temperature (4.5°C) and in eutrophication (phosphorus addition), during the crucial recruiting and growing season. We show that the addition of phosphorus alone significantly weakened the top-down effects by the cyclopoid copepod predators on their rotifer prey. In contrast, warming strengthened the top-down effects from the predator, leading to a reduction in the abundance of the rotifer prey. These effects of warming were enhanced by phosphorus addition. Together, our results demonstrate that warming made plankton prey organisms more susceptible to top-down effects from predators, but reduced their sensitivity to nutrient enrichment. In terms of the phenological effects, warming advanced the termination of diapause for both rotifers and cyclopoid copepods by about 2 weeks, but these temporal shifts, akin for both groups, resulted in no apparent trophic mismatch. Hence, from a future perspective, cyclopoid copepods are likely to benefit more from the combination of nutrient enrichment and climate warming to the detriment of their rotifer prey.
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| 10. |
- Adolfsson, Karin H., et al.
(författare)
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Scavenging of DPPH by Persistent Free Radicals in Carbonized Particles
- 2023
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Ingår i: Advanced Sustainable Systems. - : Wiley. - 2366-7486. ; 7:3
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Tidskriftsartikel (refereegranskat)abstract
- Persistent free radicals (PFR) in carbonized particles may play a role in degradation of environmental compounds. The influence of PFR is evaluated in various carbonized particles on their radical scavenging efficiency upon the common radical indicator 2-2-diphenyl-1-picrylhydrazyl (DPPH). Carbonized particles are derived by hydrothermal carbonization of glucose (C-W) or glucose and urea (NC-W) and ionothermal carbonization of glucose and urea ionic liquid (IL) (NC-IL). The carbonized materials contain OH/COOH, C=C, and C-O functionalities. The addition of urea introduces NH/NH2 functionalities. The content of polar surface groups is lower in IL-processed NC-IL. The scavenging ability, measured as DPPH UV–vis absorption decline, increases with concentration and time for all particles, while the efficiency changes are in the order of C-W > NC-W > NC-IL. Electron paramagnetic resonance analysis reveals similar radical concentration in all carbonized materials studied. The difference in efficiency is, thus, not directly related to the PFR concentration but rather to the type of PFR, surface functionalities and/or scavenging mechanism. According to the g-values, radicals in these particles are carbon-centered. The minor variation in g-values suggests interactions between the radicals and their environmental functional groups. This provides insights into the influence of PFR in carbonized materials on their radical scavenging efficiency.
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