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| 2. |
- 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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| 3. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
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| 5. |
- He, Yafang, et al.
(författare)
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Metabolomic Changes Upon Conjugated Linoleic Acid Supplementation and Predictions of Body Composition Responsiveness
- 2022
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Ingår i: Journal of Clinical Endocrinology and Metabolism. - : The Endocrine Society. - 1945-7197 .- 0021-972X. ; 107:9, s. 2606-2615
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Tidskriftsartikel (refereegranskat)abstract
- Context Conjugated linoleic acid (CLA) may optimize body composition, yet mechanisms underlining its benefits are not clear in humans. Objective We aimed to reveal the CLA-induced changes in the plasma metabolome associated with body composition improvement and the predictive performance of baseline metabolome on intervention responsiveness. Methods Plasma metabolome from overnight fasted samples at pre- and post-intervention of 65 participants in a 12-week randomized, placebo-controlled trial (3.2 g/day CLA vs 3.2 g/day sunflower oil) were analyzed using untargeted LC-MS metabolomics. Mixed linear model and machine learning were applied to assess differential metabolites between treatments, and to identify optimal panel (based on baseline conventional variables vs metabolites) predicting responders of CLA-derived body composition improvement (increased muscle variables or decreased adiposity variables) based on dual-energy x-ray absorptiometry. Results Compared with placebo, CLA altered 57 metabolites (P
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| 6. |
- 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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| 7. |
- Liu, Wenjuan, et al.
(författare)
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Strontium-Substituted Dicalcium Silicate Bone Cements with Enhanced Osteogenesis Potential for Orthopaedic Applications
- 2019
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Ingår i: Materials. - : MDPI. - 1996-1944 .- 1996-1944. ; 12:14
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Tidskriftsartikel (refereegranskat)abstract
- Incorporating Sr element in biomaterials for bone implants is an effective way to improve their biological performance, as Sr element has been proved to enhance bone regeneration and depress bone resorption activity. In the present study, we developed a Sr-incorporated dicalcium silicate (C2S) bone cement as a potential candidate for bioactive self-setting bone cement in orthopaedics and stomatology. The Sr-C2S powders containing 0.3-6.8% Sr in molar ratio were prepared by means of chemical co-precipitation, and the results of XRD analysis indicated the incorporation of Sr element into the lattice of C2S. Sr-C2S bone cements, as prepared by mixing the powders with water, have a final setting time of 570 to 594 min, and compressive strength higher than that of C2S bone cement within certain incorporation range. The Sr-C2S bone cements possessed good in vitro bioactivity by inducing apatite formation in simulated body fluid (SBF) within 7 days. Moreover, the proliferation activity of human bone marrow mesenchymal stem cells (hBMSCs) with Sr-C2S bone cements was significantly higher than that with C2S bone cement, and the alkaline phosphatase (ALP) activity of hBMSCs was also enhanced with addition of Sr element in Sr-C2S groups. The Sr-C2S might therefore be a bioactive self-setting material with enhanced biological performance and holds the prospect for application in the bone regeneration area.
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| 8. |
- Luo, Yiqi, et al.
(författare)
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Toward more realistic projections of soil carbon dynamics by Earth system models
- 2016
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Ingår i: Global Biogeochemical Cycles. - 0886-6236. ; 30:1, s. 40-56
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Tidskriftsartikel (refereegranskat)abstract
- Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool- and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. We recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure, constrain parameters, and prescribe forcing fields.
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| 9. |
- Tian, Qing, et al.
(författare)
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Short-Term Associations of Fine Particulate Matter and Synoptic Weather Types with Cardiovascular Mortality : An Ecological Time-Series Study in Shanghai, China
- 2020
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Ingår i: International Journal of Environmental Research and Public Health. - : MDPI. - 1661-7827 .- 1660-4601. ; 17:3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Exposures to both ambient fine particulate matter (PM2.5) and extreme weather conditions have been associated with cardiovascular disease (CVD) deaths in numerous epidemiologic studies. However, evidence on the associations with CVD deaths for interaction effects between PM2.5 and weather conditions is still limited. This study aimed to investigate associations of exposures to PM2.5 and weather conditions with cardiovascular mortality, and further to investigate the synergistic or antagonistic effects of ambient air pollutants and synoptic weather types (SWTs).Methods: Information on daily CVD deaths, air pollution, and meteorological conditions between 1 January 2012 and 31 December 2014 was obtained in Shanghai, China. Generalized additive models were used to assess the associations of daily PM2.5 concentrations and meteorological factors with CVD deaths. A 15-day lag analysis was conducted using a polynomial distributed lag model to access the lag patterns for associations with PM2.5.Results: During the study period, the total number of CVD deaths in Shanghai was 59,486, with a daily mean of 54.3 deaths. The average daily PM2.5 concentration was 55.0 µg/m3. Each 10 µg/m3 increase in PM2.5 concentration was associated with a 1.26% (95% confidence interval (CI): 0.40%, 2.12%) increase in CVD mortality. No SWT was statistically significantly associated with CVD deaths. For the interaction between PM2.5 and SWT, statistically significant interactions were found between PM2.5 and cold weather, with risk for PM2.5 in cold dry SWT decreasing by 1.47% (95% CI: 0.54%, 2.39%), and in cold humid SWT the risk decreased by 1.45% (95% CI: 0.52%, 2.36%). In the lag effect analysis, statistically significant positive associations were found for PM2.5 in the 1-3 lag days, while no statistically significant effects were found for other lag day periods.Conclusions: Exposure to PM2.5 was associated with short-term increased risk of cardiovascular deaths with some lag effects, while the cold weather may have an antagonistic effect with PM2.5. However, the ecological study design limited the possibility to identify a causal relationship, so prospective studies with individual level data are warranted.
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| 10. |
- Xue, Tian-Tian, et al.
(författare)
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Ignored Biodiversity in Acid Soil Islands in Karst Areas, South China : Impatiens longlinensis (Balsaminaceae), a New Critically Endangered Species
- 2020
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Ingår i: Systematic Botany. - 0363-6445 .- 1548-2324. ; 45:4, s. 891-899
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Tidskriftsartikel (refereegranskat)abstract
- The karst area in South China is notable for its fragile vegetation and unique flora with many narrow endemic species, and is one of the most threatened biodiversity hotspots in the world. However, the biodiversity of acid soil areas scattered in the karst area have previously been underestimated. With a recent increase of new discoveries of plants and animals, the conservation of biodiversity in these acid soil areas has become urgent. This study deals with a new species, Impatiens longlinensis . The new species is similar to I. yui and I. lasiophyton in having pubescence, two lateral sepals, funnelform lower sepal, and linear capsule. But it can be distinguished by having orbicular to obovate dorsal sepals and oblong to elliptic lower and upper lobes of lateral united petals. Moreover, molecular data and micro-morphological evidence also support that the species is new to science. The new species is only known from a valley near the summit of Mt. Jinzhongshan within an area of less than 5 km2. Based on the Red List categories and criteria developed by the International Union for Conservation of Nature, and the threat posed by exploitation for tourism development, we categorize it as Critically Endangered (CR).
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