| 1. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 2. |
- Patterson, Nick, et al.
(författare)
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Large-scale migration into Britain during the Middle to Late Bronze Age
- 2022
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; , s. 588-594
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Tidskriftsartikel (refereegranskat)abstract
- Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age1. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between 1000 and 875 BC, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of Iron Age people of England and Wales, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2-6. There was comparatively less gene flow from continental Europe during the Iron Age, and Britain's independent genetic trajectory is also reflected in the rise of the allele conferring lactase persistence to ~50% by this time compared to ~7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.
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| 3. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 4. |
- Adewumi, Oluseun, et al.
(författare)
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Characterization of human embryonic stem cell lines by the International Stem Cell Initiative
- 2007
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Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 25:7, s. 803-816
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Tidskriftsartikel (refereegranskat)abstract
- The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue- nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.
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| 5. |
- FitzGerald, Edward A., et al.
(författare)
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Multiplexed experimental strategies for fragment library screening using SPR biosensors
- 2020
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Surface plasmon resonance biosensor technology (SPR) is ideally suited for fragment-based lead discovery. However, generally suitable experimental procedures or detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are lacking. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. By adopting a multiplexed strategy, the range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded. We here illustrate innovative strategies using five challenging targets and variants thereof. Two libraries of 90 and 1056 fragments were screened using two different flow-based SPR biosensor systems, allowing different experimental approaches. Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted.Competing Interest StatementAnna Moberg, Maria T. Lindgren and Claes Holmgren work for Cytiva, which produce Biacore systems.
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| 6. |
- Mehra, Archit, et al.
(författare)
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Evaluation of the chemical composition of gas- and particle-phase products of aromatic oxidation
- 2020
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Ingår i: ATMOSPHERIC CHEMISTRY AND PHYSICS. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 20:16, s. 9783-9803
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Tidskriftsartikel (refereegranskat)abstract
- Aromatic volatile organic compounds (VOCs) are key anthropogenic pollutants emitted to the atmosphere and are important for both ozone and secondary organic aerosol (SOA) formation in urban areas. Recent studies have indicated that aromatic hydrocarbons may follow previously unknown oxidation chemistry pathways, including autoxidation that can lead to the formation of highly oxidised products. In this study we evaluate the gas- and particle-phase ions measured by online mass spectrometry during the hydroxyl radical oxidation of substituted C-9-aromatic isomers (1,3,5-trimethylbenzene, 1,2,4-trimethylbenzene, propylbenzene and isopropylbenzene) and a substituted polyaromatic hydrocarbon (1-methylnaphthalene) under low- and medium-NO x conditions. A time-of-flight chemical ionisation mass spectrometer (ToF-CIMS) with iodide-anion ionisation was used with a filter inlet for gases and aerosols (FIGAERO) for the detection of products in the particle phase, while a Vocus protontransfer-reaction mass spectrometer (Vocus-PTR-MS) was used for the detection of products in the gas phase. The signal of product ions observed in the mass spectra were compared for the different precursors and experimental conditions. The majority of mass spectral product signal in both the gas and particle phases comes from ions which are common to all precursors, though signal distributions are distinct for different VOCs. Gas- and particle-phase composition are distinct from one another. Ions corresponding to products contained in the near-explicit gas phase Master Chemical Mechanism (MCM version 3.3.1) are utilised as a benchmark of current scientific understanding, and a comparison of these with observations shows that the MCM is missing a range of highly oxidised products from its mechanism. In the particle phase, the bulk of the product signal from all precursors comes from ring scission ions, a large proportion of which are more oxidised than previously reported and have undergone further oxidation to form highly oxygenated organic molecules (HOMs). Under the perturbation of OH oxidation with increased NOx, the contribution of HOM-ion signals to the particle-phase signal remains elevated for more substituted aromatic precursors. Up to 43% of product signal comes from ring-retaining ions including HOMs; this is most important for the more substituted aromatics. Unique products are a minor component in these systems, and many of the dominant ions have ion formulae concurrent with other systems, highlighting the challenges in utilising marker ions for SOA.
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| 7. |
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| 8. |
- Reardon, Anthony J. F., et al.
(författare)
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Neurodevelopmental and Metabolomic Responses from Prenatal Coexposure to Perfluorooctanesulfonate (PFOS) and Methylmercury (MeHg) in Sprague-Dawley Rats
- 2019
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Ingår i: Chemical Research in Toxicology. - : American Chemical Society (ACS). - 0893-228X .- 1520-5010. ; 32:8, s. 1656-1669
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Tidskriftsartikel (refereegranskat)abstract
- Methylmercury (MeHg) and perfluoro-octanesulfonate (PFOS) are major contaminants of human blood that are both common in dietary fish, thereby raising questions about their combined impact on human development. Here, pregnant Sprague-Dawley rats ingested a daily dose, from gestational day 1 through to weaning, of either 1 mg/kg bw PFOS (PFOS-only), 1 mg/kg MeHg (MeHg-only), a mixture of 0.1 mg/kg PFOS and 1 mg/kg MeHg (Low-Mix), or of 1 mg/kg of PFOS and 1 mg/kg MeHg (High-Mix). Newborns were monitored for physical milestones and reflexive developmental responses, and in juveniles the spontaneous activity, anxiety, memory, and cognition were assessed. Targeted metabolomics of 199 analytes was applied to sectioned brain regions of juvenile offspring. Newborns in the High-Mix group had decreased weight gain as well as delayed reflexes and innate behavioral responses compared to controls and individual chemical groups indicating a toxicological interaction on early development. In juveniles, cumulative mixture effects increased in a dose-dependent manner in tests of anxiety-like behavior. However, other developmental test results suggested antagonism, as PFOS-only and MeHg-only juveniles had increased hyperactivity and thigmotaxic behavior, respectively, but fewer effects in Low-Mix and High-Mix groups. Consistent with these behavioral observations, a pattern of antagonism was also observed in neurochemicals measured in rat cortex, as PFOS-only and MeHg-only juveniles had altered concentrations of metabolites (e.g., lipids, amino acids, and biogenic amines), while no changes were evident in the combined exposures. The cortical metabolites altered in PFOS-only and MeHg-only exposed groups are involved in inhibitory and excitatory neurotransmission. These proof-of-principle findings at relatively high doses indicate the potential for toxicological interaction between PFOS and MeHg, with developmental-stage specific effects. Future mixture studies at lower doses are warranted, and prospective human birth cohorts should consider possible confounding effects from PFOS and mercury exposure on neurodevelopment.
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| 9. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 10. |
- Tan, Wen, et al.
(författare)
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Theoretical and Experimental Study on the Reaction of tert-Butylamine with OH Radicals in the Atmosphere
- 2018
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 122:18, s. 4470-4480
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 American Chemical Society. The OH-initiated atmospheric degradation of tert-butylamine (tBA), (CH 3 ) 3 CNH 2 , was investigated in a detailed quantum chemistry study and in laboratory experiments at the European Photoreactor (EUPHORE) in Spain. The reaction was found to mainly proceed via hydrogen abstraction from the amino group, which in the presence of nitrogen oxides (NO x ), generates tert-butylnitramine, (CH 3 ) 3 CNHNO 2 , and acetone as the main reaction products. Acetone is formed via the reaction of tert-butylnitrosamine, (CH 3 ) 3 CNHNO, and/or its isomer tert-butylhydroxydiazene, (CH 3 ) 3 CN=NOH, with OH radicals, which yield nitrous oxide (N 2 O) and the (CH 3 ) 3 Ċ radical. The latter is converted to acetone and formaldehyde. Minor predicted and observed reaction products include formaldehyde, 2-methylpropene, acetamide and propan-2-imine. The reaction in the EUPHORE chamber was accompanied by strong particle formation which was induced by an acid-base reaction between photochemically formed nitric acid and the reagent amine. The tert-butylaminium nitrate salt was found to be of low volatility, with a vapor pressure of 5.1 × 10 -6 Pa at 298 K. The rate of reaction between tert-butylamine and OH radicals was measured to be 8.4 (±1.7) × 10 -12 cm 3 molecule -1 s -1 at 305 ± 2 K and 1015 ± 1 hPa.
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