| 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. |
- Lawrenson, Kate, et al.
(författare)
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Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
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| 3. |
- Machiela, Mitchell J., et al.
(författare)
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Characterization of Large Structural Genetic Mosaicism in Human Autosomes
- 2015
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 96:3, s. 487-497
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.
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| 4. |
- Nik-Zainal, Serena, et al.
(författare)
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54
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Tidskriftsartikel (refereegranskat)abstract
- We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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| 5. |
- Roy, Sushmita, et al.
(författare)
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Identification of functional elements and regulatory circuits by Drosophila modENCODE.
- 2010
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 330:6012, s. 1787-1797
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Tidskriftsartikel (refereegranskat)abstract
- To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
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| 6. |
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| 7. |
- Arrhenius, Karine, et al.
(författare)
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Need for a protocol for performance evaluation of the gas analyzers used in biomethane conformity assessment
- 2024
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Ingår i: Accreditation and Quality Assurance. - : Springer Science and Business Media Deutschland GmbH. - 0949-1775 .- 1432-0517. ; 29:1, s. 69-76
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Tidskriftsartikel (refereegranskat)abstract
- Biomethane may contain trace components that can have adverse effects on gas vehicles performances and on the pipelines when injected in the gas grid. Biomethane quality assurance against specifications is therefore crucial for the integrity of the end-users’ appliances. Analytical methods used to assess biomethane conformity assessment must be validated properly and possibly, new methods specifically for biomethane should be developed. This paper provides an overview of the biomethane quality assurance infrastructure and the challenges faced with focus on sampling, analysis methods, reference gas mixtures, and performance evaluation. Currently, requirements for analytical method validation and fit-for-purpose assessments do not exist for biomethane. The industry is in urgent need of a protocol to evaluate the fit-for-purpose of methods in a harmonized manner. Reference gas mixtures to check the accuracy of the instrument and to determine the traceability of the measurement are also urgently required.
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| 8. |
- Arrhenius, Karine, et al.
(författare)
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Suitability of vessels and adsorbents for the short-term storage of biogas/biomethane for the determination of impurities – Siloxanes, sulfur compounds, halogenated hydrocarbons, BTEX
- 2017
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Ingår i: Biomass and Bioenergy. - : Elsevier BV. - 0961-9534 .- 1873-2909. ; 105, s. 127-135
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Tidskriftsartikel (refereegranskat)abstract
- Biogas is a renewable energy source with many different production pathways and various excellent opportunities to use, for example as vehicle fuel (biomethane). Reliable analytical methodologies for assessing the quality of the gas are critical to ensure that the gas can technically and safely be used. An essential part of any procedure aiming to determine the quality is the sampling and the transfer to the laboratory. One of the greatest challenges is then to ensure that the composition of the sample collected does not change between the time of sampling and the analysis. The choice of the sampling vessel to be used must be made only after fully assessing its short-term stability. In this paper, the results from short-term stability studies in different vessels (cylinders, bags and sorbents) are presented for siloxanes, BTEX, halogenated hydrocarbons and sulfur compounds. Storage of dry gas at high pressure (> 6 MPa) appears to be a good alternative however it is currently challenging to find an optimal treatment of the cylinders for all species to be assessed in biogas/biomethane. At lower pressure, adsorption effects on the inner surface of the cylinders have been observed. The use of bags and sorbent tubes also shows limitation. No existing sorbent tubes are sufficiently universal as to trap all possible impurities and high boiling compounds may adsorbed on the inner surface of the bags walls. Moreover, the presence of water when storing biogas most certainly impacts the storage stability of compounds in most vessels. Using at least two sampling methods for a given compound and comparing results will allow taking into account the eventual effects of water vapour, and adsorption on the inner surface of the vessels.
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| 9. |
- Arrhenius, Karine, et al.
(författare)
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Traceable reference gas mixtures for sulfur-free natural gas odorants
- 2014
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 13:1, s. 6695-6702
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Tidskriftsartikel (refereegranskat)abstract
- The first reference gas mixtures of sulfur-free natural gas odorants that are traceable to the International System of Units (SI) have been produced and their compositions validated. These mixtures, which contain methyl acrylate and ethyl acrylate at amount fractions between 1.1 and 2.1 μmol mol-1, can be used to underpin measurements of sulfur-free odorants, which are increasingly being used to odorize natural gas in transmission networks as they have less harmful properties than traditional sulfur-containing odorants. The reference gas mixtures produced have been shown to be stable in passivated aluminum cylinders for at least 8 months and have been validated (to within 6% or less) by interlaboratory measurements at three National Measurement Institutes. The stability of methyl acrylate and ethyl acrylate in gas sampling bags has been investigated, and the challenges of analyzing 2-ethyl-3- methylpyrazine, which is used as a stabilizer in sulfur-free odorants, are also briefly discussed.
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| 10. |
- Brown, Andrew S., et al.
(författare)
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Sampling of gaseous sulfur-containing compounds at low concentrations with a review of best-practice methods for biogas and natural gas applications
- 2015
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Ingår i: TrAC. Trends in analytical chemistry. - : Elsevier BV. - 0165-9936 .- 1879-3142. ; 64, s. 42-52
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Tidskriftsartikel (refereegranskat)abstract
- The accurate quantification of low-concentration sulfur-containing compounds is essential for the biogas and natural gas industries. We review literature data for the stability of these compounds in standard gas mixtures when sampled in cylinders with different passivations, sample bags, sorbent tubes, solid-phase microextraction and glass sampling bulbs, and we present new data obtained at our three National Measurement Institutes. We show that losses of sulfur-containing compounds are minimized when using passivated sampling cylinders, and the most suitable sorbent material for sampling these compounds is Tenax TA. We also discuss methods for transferring gas from sample vessels to analyzers and give recommendations for the selection of regulators (and other pressure-reducing devices) and transfer lines. Further, we propose approaches that could be taken to reduce or correct for losses in order to provide more accurate measurements of sulfur-containing compounds.
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