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- 2019
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Tidskriftsartikel (refereegranskat)
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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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| 4. |
- Mueller, Stefanie H., et al.
(författare)
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Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
- 2023
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Ingår i: Genome Medicine. - : BioMed Central (BMC). - 1756-994X. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.Methods: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.Results: In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 x 10(-6)) and AC058822.1 (P = 1.47 x 10(-4)), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C.Conclusions: Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 x 10(-5)), demonstrating the importance of diversifying study cohorts.
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| 5. |
- Stevens, Kristen N, et al.
(författare)
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19p13.1 is a triple negative-specific breast cancer susceptibility locus
- 2012
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Ingår i: Cancer Research. - 0008-5472 .- 1538-7445. ; 72, s. 1795-
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Tidskriftsartikel (refereegranskat)abstract
- The 19p13.1 breast cancer susceptibility locus is a modifier of breast cancer risk in BRCA1 mutation carriers and is also associated with risk of ovarian cancer. Here we investigated 19p13.1 variation and risk of breast cancer subtypes, defined by estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2) status, using 48,869 breast cancer cases and 49,787 controls from the Breast Cancer Association Consortium (BCAC). Variants from 19p13.1 were not associated with breast cancer overall or with ER-positive breast cancer but were significantly associated with ER-negative breast cancer risk [rs8170 Odds Ratio (OR)=1.10, 95% Confidence Interval (CI) 1.05 - 1.15, p=3.49 x 10-5] and triple negative (TN) (ER, PR and HER2 negative) breast cancer [rs8170 OR=1.22, 95% CI 1.13 - 1.31, p=2.22 x 10-7]. However, rs8170 was no longer associated with ER-negative breast cancer risk when TN cases were excluded [OR=0.98, 95% CI 0.89 - 1.07, p=0.62]. In addition, a combined analysis of TN cases from BCAC and the Triple Negative Breast Cancer Consortium (TNBCC) (n=3,566) identified a genome-wide significant association between rs8170 and TN breast cancer risk [OR=1.25, 95% CI 1.18 - 1.33, p=3.31 x 10-13]. Thus, 19p13.1 is the first triple negative-specific breast cancer risk locus and the first locus specific to a histological subtype defined by ER, PR, and HER2 to be identified. These findings provide convincing evidence that genetic susceptibility to breast cancer varies by tumor subtype and that triple negative tumors and other subtypes likely arise through distinct etiologic pathways.
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| 6. |
- Couch, Fergus J., et al.
(författare)
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Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
- 2016
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 7:11375, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P<5 x 10(-8)) with oestrogen receptor (ER)-negative breast cancer and BRCA1-associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5, a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (P<0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and PPIL3 at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for similar to 11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and BRCA1 breast cancer risk prediction.
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| 7. |
- Lu, Yingchang, et al.
(författare)
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A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk.
- 2018
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Ingår i: Cancer Research. - 0008-5472 .- 1538-7445. ; 78:18, s. 5419-5430
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Tidskriftsartikel (refereegranskat)abstract
- .AbstractLarge-scale genome-wide association studies (GWAS) have identified approximately 35 loci associated with epithelial ovarian cancer (EOC) risk. The majority of GWAS-identified disease susceptibility variants are located in noncoding regions, and causal genes underlying these associations remain largely unknown. Here, we performed a transcriptome-wide association study to search for novel genetic loci and plausible causal genes at known GWAS loci. We used RNA sequencing data (68 normal ovarian tissue samples from 68 individuals and 6,124 cross-tissue samples from 369 individuals) and high-density genotyping data from European descendants of the Genotype-Tissue Expression (GTEx V6) project to build ovarian and cross-tissue models of genetically regulated expression using elastic net methods. We evaluated 17,121 genes for their cis-predicted gene expression in relation to EOC risk using summary statistics data from GWAS of 97,898 women, including 29,396 EOC cases. With a Bonferroni-corrected significance level of P < 2.2 × 10−6, we identified 35 genes, including FZD4 at 11q14.2 (Z = 5.08, P = 3.83 × 10−7, the cross-tissue model; 1 Mb away from any GWAS-identified EOC risk variant), a potential novel locus for EOC risk. All other 34 significantly associated genes were located within 1 Mb of known GWAS-identified loci, including 23 genes at 6 loci not previously linked to EOC risk. Upon conditioning on nearby known EOC GWAS-identified variants, the associations for 31 genes disappeared and three genes remained (P < 1.47 × 10−3). These data identify one novel locus (FZD4) and 34 genes at 13 known EOC risk loci associated with EOC risk, providing new insights into EOC carcinogenesis.Significance: Transcriptomic analysis of a large cohort confirms earlier GWAS loci and reveals FZD4 as a novel locus associated with EOC risk. Cancer Res; 78(18); 5419–30. ©2018 AACR.
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| 8. |
- Wang, Ruifu, et al.
(författare)
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Morphology and Flow Behavior of Cellulose Nanofibers Dispersed in Glycols
- 2019
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 52:15, s. 5499-5509
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the morphology and flow behavior of cellulose nanofibers (CNFs) dispersed in organic solvents can improve the process of fabricating new cellulose-based nanocomposites. In this study, jute-based 2,2,6,6-tetramethylpiperidinyl-1-oxyl (TEMPO)-oxidized CNFs with two different charge densities (0.64 and 1.03 mmol/g) were dispersed in ethylene glycol (EG) and propylene glycol (PG) using the solvent exchange method. The morphology and dimensions of CNFs in dry and suspension states were characterized using transmission electron microscopy, atomic force microscopy, and small-angle X-ray scattering techniques. The results showed that the cross-sectional dimensions remained the same in different solvents. Rheological measurements revealed that CNF suspensions in water or glycol (EG and PG) behaved similar to typical polymer solutions with a solvent-independent overlap concentration corresponding to the crowding factor of about 14. Furthermore, a thixotropic behavior was found in the concentrated CNF/glycol systems as observed in typical CNF aqueous suspensions. The fact that TEMPO-oxidized CNFs can be well dispersed in organic solvents opens up new possibilities to improve the CNF–polymer matrix blending, where the use of a viscous solvent can delay the transition to turbulence in processing and improve the control of fiber orientation because of a slower Brownian diffusive motion.
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| 9. |
- Das, Rasel, et al.
(författare)
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Nanocellulose for Sustainable Water Purification
- 2022
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Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 122:9, s. 8936-9031
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Forskningsöversikt (refereegranskat)abstract
- Nanocelluloses (NC) are nature-based sustainable biomaterials, which not only possess cellulosic properties but also have the important hallmarks of nanomaterials, such as large surface area, versatile reactive sites or functionalities, and scaffolding stability to host inorganic nanoparticles. This class of nanomaterials offers new opportunities for a broad spectrum of applications for clean water production that were once thought impractical. This Review covers substantial discussions based on evaluative judgments of the recent literature and technical advancements in the fields of coagulation/flocculation, adsorption, photocatalysis, and membrane filtration for water decontamination through proper understanding of fundamental knowledge of NC, such as purity, crystallinity, surface chemistry and charge, suspension rheology, morphology, mechanical properties, and film stability. To supplement these, discussions on low-cost and scalable NC extraction, new characterizations including solution small-angle X-ray scattering evaluation, and structure-property relationships of NC are also reviewed. Identifying knowledge gaps and drawing perspectives could generate guidance to overcome uncertainties associated with the adaptation of NC-enabled water purification technologies. Furthermore, the topics of simultaneous removal of multipollutants disposal and proper handling of post/spent NC are discussed. We believe NC-enabled remediation nanomaterials can be integrated into a broad range of water treatments, greatly improving the cost-effectiveness and sustainability of water purification.
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| 10. |
- Geng, Lihong, et al.
(författare)
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Structure characterization of cellulose nanofiber hydrogel as functions of concentration and ionic strength
- 2017
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Ingår i: Cellulose. - : Springer Netherlands. - 0969-0239 .- 1572-882X. ; 24:12, s. 5417-5429
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Tidskriftsartikel (refereegranskat)abstract
- Carboxylated cellulose nanofibers (CNFs), having an average width of 7 nm and thickness of 1.5 nm, were produced by TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl radical)-mediated oxidation method. The fiber cross-sectional dimensions were determined using small-angle X-ray scattering (SAXS), transmission electron microscopy and atomic force microscopy techniques, where the rheological properties under different concentration and ionic strength were also investigated. The formation of hydrogel was evidenced by increasing the CNF concentration or ionic strength of the solvent (water), while the gel structure in ion-induced CNF hydrogels was found to be relatively inhomogeneous. The gelation behavior was closely related to the segmental aggregation of charged CNF, which could be quantitatively characterized by the correlation length (Ο) from the low-angle scattering profile and the scattering invariant (Q) in SAXS.
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