| 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. |
- Li, Peng, et al.
(author)
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Transcriptional reactivation of OTX2, RX1 and SIX3 during reprogramming contributes to the generation of RPE cells from human iPSCs
- 2016
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In: International Journal of Biological Sciences. - : Ivyspring International Publisher. - 1449-2288. ; 12:5, s. 505-517
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Journal article (peer-reviewed)abstract
- Directed differentiation of human induced pluripotent stem cells (iPSCs) into retinal pigmented epithelium (RPE) holds great promise in cell replacement therapy for patients suffering from degenerative eye diseases, including age-related macular degeneration (AMD). In this study, we generated iPSCs from human dermal fibroblasts (HDFs) by electroporation with episomal plasmid vectors encoding OCT4, SOX2, KLF4, L-MYC together with p53 suppression. Intriguingly, cell reprogramming resulted in a metastable transcriptional activation and selective demethylation of neural and retinal specification-associated genes, such as OTX2, RX1 and SIX3. In contrast, RPE progenitor genes were transcriptionally silent in HDFs and descendant iPSCs. Overexpression of OCT4 and SOX2 directly stimulated the expression of OTX2, RX1 and SIX3 in HDFs and iPSCs. Luciferase and chromatin immunoprecipitation (ChIP) assays further identified an OCT4- and two SOX2-binding sites located in the proximal promoter of OTX2. Histone acetylation and methylation on the local promoter also participated in the reactivation of OTX2. The transcriptional conversion of RX1 and SIX3 genes partially attributed to DNA demethylation. Subsequently, iPSCs were induced into the RPE cells displaying the characteristics of polygonal shapes and pigments, and expressing typical RPE cell markers. Taken together, our results establish readily efficient and safe protocols to produce iPSCs and iPSC-derived RPE cells, and underline that the reactivation of anterior neural transcription factor OTX2, eye field transcription factor RX1 and SIX3 in iPSCs is a feature of pluripotency acquisition and predetermines the potential of RPE differentiation.
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| 3. |
- Li, Cuiyan, et al.
(author)
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Photocatalytic and antibacterial properties of Au-decorated Fe3O4@mTiO(2) core-shell microspheres
- 2014
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In: Applied Catalysis B. - : Elsevier BV. - 0926-3373 .- 1873-3883. ; 156, s. 314-322
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Journal article (peer-reviewed)abstract
- A facile approach for the fabrication of Au-decorated mesoporous Fe3O4@TiO2 (Fe3O4@mTiO(2)) core-shell microspheres is demonstrated. The protocol involved the coating of a successive layer of TiO2 onto a magnetic Fe3O4 core via a sol-gel process, followed by TiO2 crystallization and mesopore-formation by a hydrothermal treatment, and then the deposition of Au nanoparticles onto Fe3O4@mTiO(2) microspheres through an in situ reduction of perchloric acid. The mesoporous microspheres (Fe3O4@mTiO(2)) showed stronger magnetic properties than the dense sample (Fe3O4@TiO2) before the hydrothermal treatment. The size and loading amount of Au nanoparticles were controlled by the reduction temperature and concentration of Au salt, respectively. Compared to unmodified Fe3O4@mTiO(2) microspheres, Fe3O4@mTiO(2)@Au microspheres showed higher photocatalytic activity for organic degradation and antibacterial action in water. These core-shell Fe3O4@mTiO(2)@Au microspheres can serve as efficient and recyclable photocatalysts, which have promising applications in environmental treatment.
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| 4. |
- Li, Cuiyan, et al.
(author)
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Polyacrylamide-metal nanocomposites : one-pot synthesis, antibacterial properties, and thermal stability
- 2013
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In: Journal of nanoparticle research. - : Springer Science and Business Media LLC. - 1388-0764 .- 1572-896X. ; 15:9, s. UNSP 1922-
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Journal article (peer-reviewed)abstract
- The incorporation of inorganic nanoparticles into polymers is a hot research spot, since it endows the nanocomposites with new or improved properties by exploiting synergistic effects. Here we report a facile one-pot synthesis of polyacrylamide (PAM)-metal (M = Au, Ag, or Pd) nanocomposites in ethylene glycol (EG). The simultaneous polymerization of the acylamide (AM) monomer and formation of metal nanoparticles lead to a homogeneous distribution of metal nanoparticles in the PAM matrix. The sizes of Au, Ag, and Pd nanoparticles are 55.50 +/- 10.6, 14.15 +/- 2.57, and 7.74 +/- 1.82 nm, respectively. The reaction system only includes EG, AM monomer, and corresponding metal salt. EG acts as both the solvent and the reducing reagent. Also, no initiator for AM polymerization and no surfactant for stabilization of metal nanoparticles are used. Furthermore, this simple synthetic route does not rely on any special or expensive equipment, thus can be exploited to the synthesis of similar polymer-inorganic nanocomposites. Compared to PAM, the PAM-metal nanocomposites showed enhanced thermal stability and antibacterial properties.
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| 5. |
- Li, Qian, et al.
(author)
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Multiple biomarker responses in caged benthic gastropods Bellamya aeruginosa after in situ exposure to Taihu Lake in China
- 2018
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In: Environmental Sciences Europe. - : Springer Science and Business Media LLC. - 2190-4707 .- 2190-4715. ; 30
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Journal article (peer-reviewed)abstract
- Background: Freshwater sediments have been recognized as a long-term sink and potential source for environmental pollutants released into the aquatic ecosystems. In this study, the sediment quality of Taihu Lake, which is susceptible to anthropogenic contamination, was assessed by a combination of chemical analytical and biological end points. Specifically, the snail Bellamya aeruginosa was caged in situ at two locations representing different pollution levels for different exposure times (7, 14 and 21 days). At each of these time points, biochemical parameters, i.e., phase I biotransformation enzymes ethoxyresorufin-O-deethylase (EROD), the antioxidant enzymes superoxide dismutase and catalase, reactive oxygen species, protein carbonyl content and lipid peroxidation, were evaluated in the hepato-pancreas of snails. In addition, surface sediments were collected for analysis of contaminants of concern, including inorganic pollutants, organochlorine pesticides, polychlorinated biphenyls and polybrominated diphenyl ethers.Results: Chemical analyses revealed that sediments from Taihu Lake were contaminated with trace elements and organic pollutants. Concentrations of trace elements (Cu, Ni and As) and organochlorinated pesticides (4,4'-DDE) exceeded their corresponding threshold effect level according to the sediment quality assessment values for freshwater ecosystems in Canada, indicating that adverse biological effects may occur. All biomarkers, except EROD activity, were induced in snails during all exposure times. The integrated biomarker response index (IBR) indicated that during the initial exposure phase (7 days), B. aeruginosa were subjected to significant environmental stress, which diminished during later sampling time points.Conclusions: Results showed that IBR correlated well with the levels of environmental contaminants, demonstrating the applicability of this biomonitoring approach to complex environmental exposure scenarios.
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| 6. |
- Lv, Yaodong, et al.
(author)
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Association of plaque characteristics with long-term stroke recurrence in patients with intracranial atherosclerotic disease : a 3D high-resolution MRI-based cohort study
- 2023
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In: European Radiology. - 0938-7994 .- 1432-1084.
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Journal article (peer-reviewed)abstract
- Objectives To evaluate the predictive ability of plaque characteristics for long-term stroke recurrence among patients with symptomatic intracranial atherosclerotic disease (ICAD).Methods This cohort study included 132 patients with acute ischemic stroke (AIS) attributed to ICAD who were recruited between July 2017 and December 2020 and followed until stroke recurrence or December 2021. Plaque surface irregularity, degree of stenosis, plaque burden, remodeling ratio, enhancement ratio, and intraplaque hemorrhage were assessed with 3-dimensional high-resolution magnetic resonance vessel wall imaging (3D HR-MRI). Data were analyzed using Cox models, receiver operating characteristic (ROC) curves, and Kaplan-Meier survival analysis.Results Of the 132 patients, during a median follow-up of 2.8 years, stroke recurrence occurred in 35 patients. The multivariable-adjusted hazard ratio (95% confidence interval) of stroke recurrence was 3.15 (1.34-7.42) per 10% increase in plaque burden and 2.17 (1.27-3.70) for enhancement ratio. The area under the curve (AUC) to predict stroke recurrence was 0.725 (95% CI 0.629-0.822) for plaque burden, 0.692 (95% CI 0.593-0.792) for enhancement ratio, and only 0.595 (95% CI 0.492-0.699) for the Essen stroke risk score. The Kaplan-Meier survival analysis further demonstrated significant differences in survival of free recurrent stroke between patients with plaque burden or enhancement ratio below and above the optimum cut-offs (both p < 0.001).Conclusion Higher plaque burden and enhancement ratio are independent risk factors for long-term stroke recurrence among patients with symptomatic ICAD, and valuable imaging markers for predicting and stratifying risk of stroke recurrence.
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| 7. |
- Ma, Yuanjun, et al.
(author)
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Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells
- 2016
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In: SpringerPlus. - : Springer Science and Business Media LLC. - 2193-1801. ; 5
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Journal article (peer-reviewed)abstract
- Docetaxel has been the standard first-line therapy in metastatic castration resistant prostate cancer. The survival benefit is, however, limited by either primary or acquired resistance. In this study, Du145 prostate cancer cells were converted to docetaxel-resistant cells Du145-R and Du145-RB by in vitro culturing. Next generation RNAseq was employed to analyze these cell lines. Forty-two genes were identified to have acquired mutations after the resistance development, of which thirty-four were found to have mutations in published sequencing studies using prostate cancer samples from patients. Fourteen novel and 2 previously known fusion genes were inferred from the RNA-seq data, and 13 of these were validated by RT-PCR and/or re-sequencing. Four in-frame fusion transcripts could be transcribed into fusion proteins in stably transfected HEK293 cells, including MYH9-EIF3D and LDLR-RPL31P11, which were specific identified or up-regulated in the docetaxel resistant DU145 cells. A panel of 615 gene transcripts was identified to have significantly changed expression profile in the docetaxel resistant cells. These transcriptional changes have potential for further study as predictive biomarkers and as targets of docetaxel treatment.
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| 8. |
- Yin, Ge, et al.
(author)
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Spatial distribution and bioaccumulation of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in snails (Bellamya aeruginosa) and sediments from Taihu Lake area, China
- 2017
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In: Environmental Science and Pollution Research. - : SPRINGER HEIDELBERG. - 0944-1344 .- 1614-7499. ; 24:8, s. 7740-7751
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Journal article (peer-reviewed)abstract
- Taihu Lake area is one of the densest metropolitan areas in the world including diverse industrial activity. In the present study, the snail (Bellamya aeruginosa) and sediment were collected from the Taihu Lake area to investigate the contamination status, congener pattern, spatial distribution, and bioaccumulation effect of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). The samples underwent liquid extraction, lipid removal by sulfuric acid, and acidic silica gel column, and subsequently analyzed by gas chromatography-electron capture detector (GC-ECD) and gas chromatography-mass spectrometry (GC-MS). Concentration of S22PCBs ranged between 90 and 680 ng g(-1) lipid weight in the snails and between 0.018 and 0.82 ng g(-1) dry weight in the sediments. Concentration of S24PBDEs varied from 25 to 200 ng g(-1) lipid weight in the snails and from 0.62 to 67 ng g(-1) dry weight in the sediments. The levels of PCBs and PBDEs observed were in the medium to low range compared with other studies in the world. CB-153 was the predominant PCB congener in both snails and sediments whereas BDE-209 showed a low bioavailability in the snails, even if it contributed up to 70% of S24PBDEs in the sediments. The spatial distribution showed that the highest concentration of PCBs and PBDEs were detected in samples from Zhushan Lake. East Taihu Lake and Dianshan Lake showed lower concentration of PCBs and PBDEs than the other sampling sites. Biota-sediment accumulation was found between snails and sediments of most of PCB and PBDE congeners except for the highly brominated BDEs (i.e., BDE-209). Therefore, sediment is suggested to be an appropriate matrix to monitor BDE-209 while aquatic species such as the snail could be good for monitoring of PCBs and lower brominated BDE congeners. No significant correlation (Spearman correlation test, two-tailed) of CB-153 (r = 0.54, p = 0.27) or BDE-47 (r = 0.60, p = 0.21) was found between snails and sediments.
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| 9. |
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| 10. |
- Zhou, Yihui, et al.
(author)
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Human exposure to PCDDs and their precursors from heron and tern eggs in the Yangtze River Delta indicate PCP origin
- 2017
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In: Environmental Pollution. - : Elsevier BV. - 0269-7491 .- 1873-6424. ; 225, s. 184-192
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Journal article (peer-reviewed)abstract
- Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are highly toxic to humans and wildlife. In the present study, PCDD/Fs were analyzed in the eggs of whiskered terns (Chlidonias hybrida), and genetically identified eggs from black-crowned night herons (Nycticorax nycticorax) sampled from two lakes in the Yangtze River Delta area, China. The median toxic equivalent (TEQ) of PCDD/Fs were 280 (range: 95-1500) and 400 (range: 220-1100) pg TEQ g(-1) lw (WHO, 1998 for birds) in the eggs of black-crowned night heron and whiskered tern, respectively. Compared to known sources, concentrations of PCDDs relative to the sum of PCDD/Fs in bird eggs, demonstrated high abundance of octachlorodibenzo-p-dioxin (OCDD), 1,2,3,4,6,7,8-heptaCDD and 1,2,3,6,7,8-hexaCDD indicating pentachlorophenol (PCP), and/or sodium pentachlorophenolate (Na-PCP) as significant sources of the PCDD/Fs. The presence of polychlorinated diphenyl ethers (PCDEs), hydroxylated and methoxylated polychlorinated diphenyl ethers (OH-and Me0-PCDEs, known impurities in PCP products), corroborates this hypothesis. Further, significant correlations were found between the predominant congener CDE-206, 3'-OH-CDE-207, 2'-MeO-CDE-206 and OCDD, indicating a common origin. Eggs from the two lakes are sometimes used for human consumption. The WHO health-based tolerable intake of PCDD/Fs is exceeded if eggs from the two lakes are consumed regularly on a weekly basis, particularly for children. The TEQs extensively exceed maximum levels for PCDD/Fs in hen eggs and egg products according to EU legislation (2.5 pg TEQ g(-1)/w). The results suggest immediate action should be taken to manage the contamination, and further studies evaluating the impacts of egg consumption from wild birds in China. Likewise, studies on dioxins and other POPs in common eggs need to be initiated around China.
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