| 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. |
- Guo, Xingyi, et al.
(författare)
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Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects
- 2020
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Ingår i: Gastroenterology. - : Elsevier. - 0016-5085 .- 1528-0012. ; 160:4, s. 1164-1178
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Tidskriftsartikel (refereegranskat)abstract
- Background and Aims: Susceptibility genes and the underlying mechanisms for the majority of risk loci identified by genome-wide association studies (GWAS) for colorectal cancer (CRC) risk remain largely unknown. We conducted a transcriptome-wide association study (TWAS) to identify putative susceptibility genes.Methods: Gene-expression prediction models were built using transcriptome and genetic data from the 284 normal transverse colon tissues of European descendants from the Genotype-Tissue Expression (GTEx), and model performance was evaluated using data from The Cancer Genome Atlas (n = 355). We applied the gene-expression prediction models and GWAS data to evaluate associations of genetically predicted gene-expression with CRC risk in 58,131 CRC cases and 67,347 controls of European ancestry. Dual-luciferase reporter assays and knockdown experiments in CRC cells and tumor xenografts were conducted.Results: We identified 25 genes associated with CRC risk at a Bonferroni-corrected threshold of P < 9.1 × 10-6, including genes in 4 novel loci, PYGL (14q22.1), RPL28 (19q13.42), CAPN12 (19q13.2), MYH7B (20q11.22), and MAP1L3CA (20q11.22). In 9 known GWAS-identified loci, we uncovered 9 genes that have not been reported previously, whereas 4 genes remained statistically significant after adjusting for the lead risk variant of the locus. Through colocalization analysis in GWAS loci, we additionally identified 12 putative susceptibility genes that were supported by TWAS analysis at P < .01. We showed that risk allele of the lead risk variant rs1741640 affected the promoter activity of CABLES2. Knockdown experiments confirmed that CABLES2 plays a vital role in colorectal carcinogenesis.Conclusions: Our study reveals new putative susceptibility genes and provides new insight into the biological mechanisms underlying CRC development.
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| 3. |
- Shen, Qian, et al.
(författare)
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The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis
- 2018
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Ingår i: Molecular Plant. - : Cell Press. - 1674-2052 .- 1752-9867. ; 11:6, s. 776-788
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Tidskriftsartikel (refereegranskat)abstract
- Artemisia annua, commonly known as sweet wormwood or Qinghao, is a shrub native to China and has long been used for medicinal purposes. A. annua is now cultivated globally as the only natural source of a potent anti-malarial compound, artemisinin. Here, we report a high-quality draft assembly of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species. We found that, as one of a few sequenced genomes in the Asteraceae, the A. annua genome contains a large number of genes specific to this large angiosperm clade. Notably, the expansion and functional diversification of genes encoding enzymes involved in terpene biosynthesis are consistent with the evolution of the artemisinin biosynthetic pathway. We further revealed by transcriptome profiling that A. annua has evolved the sophisticated transcriptional regulatory networks underlying artemisinin biosynthesis. Based on comprehensive genomic and transcriptomic analyses we generated transgenic A. annua lines producing high levels of artemisinin, which are now ready for large-scale production and thereby will help meet the challenge of increasing global demand of artemisinin.
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| 4. |
- Su, Changqing, et al.
(författare)
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Gene-Viral Cancer Therapy Using Dual-Regulated Oncolytic Adenovirus with Antiangiogenesis Gene for Increased Efficacy.
- 2008
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Ingår i: Molecular Cancer Research. - 1557-3125. ; 6, s. 568-575
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Tidskriftsartikel (refereegranskat)abstract
- Conditionally replicative adenovirus (CRAD) represents a promising approach for cancer therapy. Several CRADs controlled by the human telomerase reverse transcriptase promoter have been developed. However, because of their replicative capacity, the importance of cancer specificity for CRADs needs to be further emphasized. In this study, we have developed a novel dual-regulated CRAD, CNHK500-mE, which has its E1a and E1b gene controlled by the human telomerase reverse transcriptase promoter and the hypoxia response element, respectively. It also carries a mouse endostatin expression cassette controlled by the cytomegalovirus promoter. These properties allow for increased cancer cell targeting specificity and decreased adverse side effects. We showed that CNHK500-mE preferentially replicated in cancer cells. Compared with a replication-defective vector carrying the same endostatin expression cassette, CNHK500-mE-mediated transgene expression level was markedly increased via viral replication within cancer cells. In the nasopharyngeal tumor xenograft model, CNHK500-mE injection resulted in antitumor efficacy at day 7 after therapy. Three weeks later, it led to significant inhibition of xenograft tumor growth due to the combined effects of viral oncolytic therapy and antiangiogenesis gene therapy. Pathologic examination showed that most cancer cells were positive for adenoviral capsid protein and for apoptotic terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling in the CNHK500-mE-treated tumor tissues, and the microvessels in these tumor tissues were diminished in quantity and abnormal in morphology. These results suggest that, as a potential cancer therapeutic agent, the CNHK500-mE is endowed with higher specificity to cancer cells and low cytotoxicity to normal cells. (Mol Cancer Res 2008;6(4):OF1-8).
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| 5. |
- Sun, Yan, et al.
(författare)
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Metal-free Se-based tetra-doped carbon catalyst for high-selective electro-reduction of CO2 into CO
- 2023
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Ingår i: Journal of Environmental Chemical Engineering. - 2213-3437. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- In electrocatalytic CO2 reduction reaction (CO2RR), metal-free Se-based multi-doping carbon has become a new focus. In this paper, a series of metal-free Se, B, P, N doped carbon-based catalysts (Se-BP-N-C) were prepared by a simple and scalable pyrolysis method. The electrocatalytic CO2 reduction results show that, the main product on Se-BP-N-C catalyst is CO, and there are no other by-products except H2. Specifically, the optimal one prepared at 1050 °C (named Se-BP-N-C (1050)), can selectively reduce CO2 into CO with Faradaic efficiency (FE) up to 96.2% (at − 0.5 V), and maintains long-term stability after continuous electrolysis for 10 h in a flow cell (current density remained 82.7%). This study would provide a good reference for designing advanced efficient metal-free catalysts in electrocatalysis.
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| 6. |
- Wang, Yong, et al.
(författare)
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Assessment of CAR- or CD46-Dependent Adenoviral Vector-Mediated TRAIL Gene Therapy in Clinical Adenocarcinoma Lung Cancer Cells
- 2009
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Ingår i: Oncology. - : S. Karger AG. - 1423-0232 .- 0030-2414. ; 77:6, s. 366-377
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Tidskriftsartikel (refereegranskat)abstract
- Adenoviral vector-mediated transfer of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) can be a powerful approach to lung cancer therapy. However, the efficiency of adenoviral vector gene transfer and the sensitivity to TRAIL-induced apoptosis in the context of adenoviral vector gene transfer have yet to be characterized in primary lung cancers. In this study, we investigated the expression of adenoviral receptor CD46 expression in primary lung cancer cells. In contrast to previous reports on enhanced CD46 expression in various types of cancer cells, we show a significantly higher CD46 expression in lung adenocarcinomas compared to lung squamous cell carcinomas. Using Ad5-GFP and Ad5F35-GFP vectors, we demonstrated an improved gene transfer efficiency in primary lung cancer cells by the Ad5F35 vector. The apoptosis induction effect mediated by Ad5-TRAIL and Ad5F35-TRAIL vector gene transfer was compared in cells from 10 lung adenocarcinomas. Of 5 lung cancers in which apoptosis was induced, 2 had an enhanced effect by Ad5F35-TRAIL vector gene transfer compared to Ad5-GFP. Thus, these results indicate a method to identify TRAIL-sensitive primary lung cancers, which will also facilitate the analysis of resistance mechanisms in lung cancers. Copyright (C) 2010 S. Karger AG, Basel
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| 7. |
- Wang, Yong, et al.
(författare)
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Coxsackievirus and adenovirus receptor expression in non-malignant lung tissues and clinical lung cancers
- 2006
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Ingår i: Journal of Molecular Histology. - : Springer Science and Business Media LLC. - 1567-2379 .- 1567-2387. ; 37:3-4, s. 153-160
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Tidskriftsartikel (refereegranskat)abstract
- Adenoviral vector mediated gene delivery has been applied in clinical trials and mechanistic studies to explore new treatment approaches for lung cancers. The expression of coxsackievirus adenovirus receptor (CAR), the primary receptor for the most commonly used adenovirus serotype 5 (Ad5)-based vectors, predominantly determines the permissiveness of lung cancer cells. CAR expression is also suggested to modulate tumor cell proliferation capacity. Here, we studied CAR expression in archival lung cancer specimens by using well-characterized CAR 72 antibodies. High levels of CAR expression were observed in most of the 32 cases of squamous cell carcinoma lung cancers and in all the five cases of small cell lung cancers investigated. In contrast, high levels of CAR expression were detected only in 6 of 22 adenocarcinoma lung cancers. The relative levels of CAR expression did not correlate with the pathologic grade in lung cancers, and was thus inconsistent with a role of modulating cancer cell proliferation. Of note, CAR expression was not detected in non-malignant alveolar cells. Our data suggest a preferred utility of Ad5 vector mediated gene delivery to squamous cell carcinoma lung cancers, small cell lung cancers, but not to the majority of adenocarcinoma lung cancers.
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| 8. |
- Zhou, Yongqiang, et al.
(författare)
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How hydrology and anthropogenic activity influence the molecular composition and export of dissolved organic matter : Observations along a large river continuum
- 2021
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Ingår i: Limnology and Oceanography. - : John Wiley & Sons. - 0024-3590 .- 1939-5590. ; 66:5, s. 1730-1742
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Tidskriftsartikel (refereegranskat)abstract
- Large rivers are the main arteries for transportation of carbon to the ocean; yet, how hydrology and anthropogenic disturbances may change the composition and export of dissolved organic matter along large river continuums is largely unknown. The Yangtze River has a watershed area of 1.80 x 10(6) km(2). It originates from the Qinghai-Tibet Plateau and flows 6300 km eastward through the center of China. We collected samples (n = 271) along the river continuum and analyzed weekly samples at the most downstream situated gauging station in 2017-2018 and gathered long-term (2006-2018) water quality data. We found higher gross domestic product, population density, and urban and agricultural land use downstream than upstream of the Three Gorges Dam, coinciding with higher dissolved organic carbon (DOC), UV absorption (a(254)), specific ultraviolet absorbance (SUVA(254)), parallel factor analysis-derived C1-C5, aliphatic compounds, and lower a(250):a(365) and spectral slope (S275-295). Chemical oxygen demand, humic-like C1-C2 and C6, and protein-like C4 and C7 increased, while dissolved oxygen and ammonium decreased with increasing discharge at most of the sites studied, including the intensively monitored downstream site. The annual DOC fluxes were ca. 1.5-1.8 Tg yr(-1), and 12-18% was biodegradable in a 28-d bio-incubation. Our results highlight that urbanization and stormwater periods enhanced the export of both terrestrial organic-rich substances and household effluents from nearshore residential areas. Our study emphasizes the continued need to protect the Yangtze River watershed as increased organic carbon loading or altered composition and bio-lability may change the ecosystem function and carbon cycling.
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| 9. |
- Allgurén, Thomas, 1986, et al.
(författare)
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Alkali sulfation during combustion of coal in a pilot scale facility using additives to alter the global sulfur to potassium and chlorine to potassium ratios
- 2021
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Ingår i: Proceedings of the Combustion Institute. - : Elsevier BV. - 1540-7489. ; 38:3, s. 4171-4178
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Tidskriftsartikel (refereegranskat)abstract
- Due to the urgent needs to reduce anthropogenic carbon dioxide emissions there is an increasing interest in the use of alternative fuels. For this reason, there is a need for new knowledge on how to design and adapt existing heat and power plants to biogenic and waste-derived fuels. This work relates to co-firing of biomass and coal and the sulfation of alkali chlorides in coal-fired flames doped with chemical additives. We aim to examine the global time scales of alkali sulfation and chlorination based on combustion experiments that were conducted in a 30-kW coal flame. Temperature, gas and particle composition measurements were conducted. Both experiments and modelling support that the apparent alkali sulfation kinetics are fast in a coal-fired flame and that it is dominated entirely by the presence of SO 2. The availability of oxygen and carbon monoxide, or hydrocarbons, is also critical to sustain the sulfation reaction cycle; low concentrations are sufficient. For industrial boilers this implies that sulfur addition, in combination with reburning, should constitute an efficient strategy to mitigate alkali-chlorination and the related high temperature corrosion.
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| 10. |
- Allgurén, Thomas, 1986, et al.
(författare)
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The Influence of Alkali, Chlorine and Sulfur on Aerosol Formation
- 2019
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The use of low-quality fuels in power generation is typically motivated by a potential reduction in fuel costs or CO2 emissions, the latter in case the fuel is based on biomass. These features make low quality fuels attractive at the same time as such fuels are usually problematic to use in power generation due to fuel composition. One of the main issues is deposition of aerosols upon heating surfaces reducing heat transfer and causing high-temperature corrosion (HTC). The later most often related to alkali chlorides, and these are formed from alkali species and chlorine when released during the combustion process. The present work aims to investigate how the gas phase chemistry are connected to the formation aerosols and their characteristics. This is an ongoing work why only part of the preliminary results is presented focusing on the interaction between alkali, sulfur and chlorine in the gas phase. The results presented here indicate a clear correlation between the S/Cl ratio and the formation of alkali sulfates over chlorides. It is also indicated that the local conditions at which the species are released and available in the gas phase is important for the resulting formation of alkali sulfates.
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