| 21. |
- Pope, Welkin H, et al.
(författare)
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Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.
- 2015
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Ingår i: eLIFE. - 2050-084X. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.
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| 22. |
- Stephens, Lucas, et al.
(författare)
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Archaeological assessment reveals Earth’s early transformation through land use
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 365:6456, s. 897-902
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Tidskriftsartikel (refereegranskat)abstract
- Humans began to leave lasting impacts on Earth’s surface starting 10,000 to 8000 years ago. Through a synthetic collaboration with archaeologists around the globe, Stephens et al. compiled a comprehensive picture of the trajectory of human land use worldwide during the Holocene (see the Perspective by Roberts). Hunter-gatherers, farmers, and pastoralists transformed the face of Earth earlier and to a greater extent than has been widely appreciated, a transformation that was essentially global by 3000 years before the present.Science, this issue p. 897; see also p. 865Environmentally transformative human use of land accelerated with the emergence of agriculture, but the extent, trajectory, and implications of these early changes are not well understood. An empirical global assessment of land use from 10,000 years before the present (yr B.P.) to 1850 CE reveals a planet largely transformed by hunter-gatherers, farmers, and pastoralists by 3000 years ago, considerably earlier than the dates in the land-use reconstructions commonly used by Earth scientists. Synthesis of knowledge contributed by more than 250 archaeologists highlighted gaps in archaeological expertise and data quality, which peaked for 2000 yr B.P. and in traditionally studied and wealthier regions. Archaeological reconstruction of global land-use history illuminates the deep roots of Earth’s transformation and challenges the emerging Anthropocene paradigm that large-scale anthropogenic global environmental change is mostly a recent phenomenon.
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| 23. |
- Turcot, Valerie, et al.
(författare)
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Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity
- 2018
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:1, s. 26-41
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are similar to 10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed similar to 7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
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| 24. |
- Wang, Li-San, et al.
(författare)
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Rarity of the Alzheimer Disease-Protective APP A673T Variant in the United States.
- 2015
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Ingår i: JAMA neurology. - : American Medical Association (AMA). - 2168-6157 .- 2168-6149. ; 72:2
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Tidskriftsartikel (refereegranskat)abstract
- Recently, a rare variant in the amyloid precursor protein gene (APP) was described in a population from Iceland. This variant, in which alanine is replaced by threonine at position 673 (A673T), appears to protect against late-onset Alzheimer disease (AD). We evaluated the frequency of this variant in AD cases and cognitively normal controls to determine whether this variant will significantly contribute to risk assessment in individuals in the United States.
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| 25. |
- Wang, Wenli, et al.
(författare)
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Evaluation of air-soil temperature relationships simulated by land surface models during winter across the permafrost region
- 2016
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Ingår i: Cryosphere. - : Copernicus GmbH. - 1994-0416. ; 10:4, s. 1721-1737
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Tidskriftsartikel (refereegranskat)abstract
- A realistic simulation of snow cover and its thermal properties are important for accurate modelling of permafrost. We analyse simulated relationships between air and near-surface (20 cm) soil temperatures in the Northern Hemisphere permafrost region during winter, with a particular focus on snow insulation effects in nine land surface models, and compare them with observations from 268 Russian stations. There are large cross-model differences in the simulated differences between near-surface soil and air temperatures (ΔT; 3 to 14 °C), in the sensitivity of soil-to-air temperature (0.13 to 0.96 °C °C-1), and in the relationship between ΔT and snow depth. The observed relationship between ΔT and snow depth can be used as a metric to evaluate the effects of each model's representation of snow insulation, hence guide improvements to the model's conceptual structure and process parameterisations. Models with better performance apply multilayer snow schemes and consider complex snow processes. Some models show poor performance in representing snow insulation due to underestimation of snow depth and/or overestimation of snow conductivity. Generally, models identified as most acceptable with respect to snow insulation simulate reasonable areas of near-surface permafrost (13.19 to 15.77 million km2). However, there is not a simple relationship between the sophistication of the snow insulation in the acceptable models and the simulated area of Northern Hemisphere near-surface permafrost, because several other factors, such as soil depth used in the models, the treatment of soil organic matter content, hydrology and vegetation cover, also affect the simulated permafrost distribution.
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| 26. |
- Xia, Jianyang, et al.
(författare)
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Terrestrial ecosystem model performance in simulating productivity and its vulnerability to climate change in the northern permafrost region
- 2017
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Ingår i: Journal of Geophysical Research - Biogeosciences. - 2169-8953. ; 122:2, s. 430-446
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Tidskriftsartikel (refereegranskat)abstract
- Realistic projection of future climate-carbon (C) cycle feedbacks requires better understanding and an improved representation of the C cycle in permafrost regions in the current generation of Earth system models. Here we evaluated 10 terrestrial ecosystem models for their estimates of net primary productivity (NPP) and responses to historical climate change in permafrost regions in the Northern Hemisphere. In comparison with the satellite estimate from the Moderate Resolution Imaging Spectroradiometer (MODIS; 246±6gCm-2yr-1), most models produced higher NPP (309±12gCm-2yr-1) over the permafrost region during 2000-2009. By comparing the simulated gross primary productivity (GPP) with a flux tower-based database, we found that although mean GPP among the models was only overestimated by 10% over 1982-2009, there was a twofold discrepancy among models (380 to 800gCm-2yr-1), which mainly resulted from differences in simulated maximum monthly GPP (GPPmax). Most models overestimated C use efficiency (CUE) as compared to observations at both regional and site levels. Further analysis shows that model variability of GPP and CUE are nonlinearly correlated to variability in specific leaf area and the maximum rate of carboxylation by the enzyme Rubisco at 25°C (Vcmax_25), respectively. The models also varied in their sensitivities of NPP, GPP, and CUE to historical changes in climate and atmospheric CO2 concentration. These results indicate that model predictive ability of the C cycle in permafrost regions can be improved by better representation of the processes controlling CUE and GPPmax as well as their sensitivity to climate change.
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