| 1. |
- Wessel, Jennifer, et al.
(författare)
-
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
- 2015
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Fasting glucose and insulin are intermediate traits for type 2 diabetes. Here we explore the role of coding variation on these traits by analysis of variants on the HumanExome BeadChip in 60,564 non-diabetic individuals and in 16,491 T2D cases and 81,877 controls. We identify a novel association of a low-frequency nonsynonymous SNV in GLP1R (A316T; rs10305492; MAF = 1.4%) with lower FG (beta = -0.09 +/- 0.01 mmol l(-1), P = 3.4 x 10(-12)), T2D risk (OR[95% CI] = 0.86[0.76-0.96], P = 0.010), early insulin secretion (beta = -0.07 +/- 0.035 pmol(insulin) mmol(glucose)(-1), P = 0.048), but higher 2-h glucose (beta = 0.16 +/- 0.05 mmol l(-1), P = 4.3 x 10(-4)). We identify a gene-based association with FG at G6PC2 (p(SKAT) = 6.8 x 10(-6)) driven by four rare protein-coding SNVs (H177Y, Y207S, R283X and S324P). We identify rs651007 (MAF = 20%) in the first intron of ABO at the putative promoter of an antisense lncRNA, associating with higher FG (beta = 0.02 +/- 0.004 mmol l(-1), P = 1.3 x 10(-8)). Our approach identifies novel coding variant associations and extends the allelic spectrum of variation underlying diabetes-related quantitative traits and T2D susceptibility.
|
|
| 2. |
- Marouli, Eirini, et al.
(författare)
-
Rare and low-frequency coding variants alter human adult height
- 2017
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 542:7640, s. 186-190
-
Tidskriftsartikel (refereegranskat)abstract
- Height is a highly heritable, classic polygenic trait with approximately 700 common associated variants identified through genome-wide association studies so far. Here, we report 83 height-associated coding variants with lower minor-allele frequencies (in the range of 0.1-4.8%) and effects of up to 2 centimetres per allele (such as those in IHH, STC2, AR and CRISPLD2), greater than ten times the average effect of common variants. In functional follow-up studies, rare height increasing alleles of STC2 (giving an increase of 1-2 centimetres per allele) compromised proteolytic inhibition of PAPP-A and increased cleavage of IGFBP-4 in vitro, resulting in higher bioavailability of insulin-like growth factors. These 83 height-associated variants overlap genes that are mutated in monogenic growth disorders and highlight new biological candidates (such as ADAMTS3, IL11RA and NOX4) and pathways (such as proteoglycan and glycosaminoglycan synthesis) involved in growth. Our results demonstrate that sufficiently large sample sizes can uncover rare and low-frequency variants of moderate-to-large effect associated with polygenic human phenotypes, and that these variants implicate relevant genes and pathways.
|
|
| 3. |
- Scott, Robert A., et al.
(författare)
-
An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans
- 2017
-
Ingår i: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 66:11, s. 2888-2902
-
Tidskriftsartikel (refereegranskat)abstract
- To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 x 10(-8)), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.
|
|
| 4. |
- Turcot, Valerie, et al.
(författare)
-
Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity
- 2018
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:1, s. 26-41
-
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.
|
|
| 5. |
- Kurilshikov, Alexander, et al.
(författare)
-
Large-scale association analyses identify host factors influencing human gut microbiome composition
- 2021
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 53:2, s. 156-165
-
Tidskriftsartikel (refereegranskat)abstract
- To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 x 10(-8)) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 x 10(-20)), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 x 10(-10) < P < 5 x 10(-8)) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.
|
|
| 6. |
- Jensen, Torben R., et al.
(författare)
-
Versatile in situ powder X-ray diffraction cells for solid-gas investigations
- 2010
-
Ingår i: Journal of Applied Crystallography. - 1600-5767. ; 43, s. 1456-1463
-
Tidskriftsartikel (refereegranskat)abstract
- This paper describes new sample cells and techniques for in situ powder X-ray diffraction specifically designed for gas absorption studies up to ca 300 bar (1 bar = 100 000 Pa) gas pressure. The cells are for multipurpose use, in particular the study of solid-gas reactions in dosing or flow mode, but can also handle samples involved in solid-liquid-gas studies. The sample can be loaded into a single-crystal sapphire (Al2O3) capillary, or a quartz (SiO2) capillary closed at one end. The advantages of a sapphire single-crystal cell with regard to rapid pressure cycling are discussed, and burst pressures are calculated and measured to be similar to 300 bar. An alternative and simpler cell based on a thin-walled silicate or quartz glass capillary, connected to a gas source via a VCR fitting, enables studies up to similar to 100 bar. Advantages of the two cell types are compared and their applications are illustrated by case studies.
|
|
| 7. |
- Mosegaard, Lene, et al.
(författare)
-
Reactivity of LiBH4: In situ synchrotron radiation powder X-ray diffraction study
- 2008
-
Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 112:4, s. 1299-1303
-
Tidskriftsartikel (refereegranskat)abstract
- Lithium tetrahydridoboranate (LiBH4) may be a potentially interesting material for hydrogen storage, but in order to absorb and desorb hydrogen routinely and reversibly, the kinetics and thermodynamics need to be improved significantly. A priori, this material has one of the highest theoretical gravimetric hydrogen contents, 18.5 wt%, but unfortunately for practical applications, hydrogen release occurs at too high temperature in a non-reversible way. By means of in situ synchrotron radiation powder X-ray diffraction (SR-PXD), the interaction between LiBH4 and different additives-SiO2, TiCl3, LiCl, and Au - is investigated. It is found that silicon dioxide reacts with molten LiBH4 and forms Li2SiO3 or Li4SiO4 at relatively low amounts of SiO2, e.g., with 5.0 and 9.9 mol % SiO2 in LiBH4, Whereas, for higher amounts of SiO2 (e.g., 25.5 mol %), only the Li2SiO3 phase is observed. Furthermore, we demonstrate that a solid-state reaction occurs between LiBH4 and TiCl3 to form LiCl at room temperature. At elevated temperatures, more LiCl is formed simultaneously with a decrease in the diffracted intensity from TiCl3. Lithium chloride shows some solubility in solid LiBH4 at T > 100 degrees C. This is the first report of substituents that accommodate the structure of LiBH4 by a solid/solid dissolution reaction. Gold is found to react with molten LiBH4 forming a Li-Au alloy with CuAu3-type structure. These studies demonstrate that molten LiBH4 has a high reactivity, and finding a catalyst for this H-rich system may be a challenge.
|
|
| 8. |
- Arnbjerg, Lene M., et al.
(författare)
-
Structure and Dynamics for LiBH4-LiCl Solid Solutions
- 2009
-
Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 21:24, s. 5772-5782
-
Tidskriftsartikel (refereegranskat)abstract
- A Surprisingly high degree of structural and compositional dynamics is observed in the system LiBH4-LiCl as a function of temperature and time. Rietveld refinement of synchrotron radiation powder X-ray diffraction (SR-PXD) data reveals that Cl- readily substitutes for BH4- in the Structure of LiBH4. Prolonged heating a sample of LiBH4-LiCl (1:1 molar ratio) above the phase transition temperature and below the melting point (108 < T < 275 degrees C) can produce highly chloride substituted hexagonal lithium borohydride, h-Li(BH4)(l-x)Cl-x, e.g., x similar to 0.42, after heating from room temperature (RT) to 224 degrees C at 2.5 degrees C/min. LiCl has a higher solubility in h-LiBH4 its compared to orthorhombic lithium borohydride, o-LiBH4, which is illustrated by a LiBH4-LiCl (1:1) sample equilibrated at 245 degrees C for 24 days and left at RT for another 13 months. Rietveld refinement reveals that this sample contains o-Li(BH4)(0.91)Cl-0.09 and LiCl. This illustrates a significantly faster dissolution of LiCl in h-LiBH4 its compared to a slower segregation of LiCl from o-LiBH4, which is also demonstrated by in situ SR-PXD from three cycles of heating and cooling of the same Li(BH4)(0.91)Cl-0.09 sample. The substitution of the smaller Cl- for the larger BH4- ion is clearly observed as a reduction in the unit cell volume as a function of time and temperature. A significant stabilization of h-LiBH4 is found to depend on the degree of anion substitution. Variable temperature solid-state magic-angle spinning (MAS) Li-7 and B-13 NMR experiments oil pure LiBH4 show an increase in full width at half maximum (fwhm) when approaching the phase transition from o- to h-LiBH4, which indicates an increase of the relaxation rate (i.e. T-2 decreases). A less pronounced effect is observed for ion-substituted Li(BH4)(1-x)Cl-x, 0.09 < x < 0.42. The MAS NMR experiments also demonstrate a higher degree of motion in the hexagonal phase, i.e., fwhm is reduced by more than a Factor of 10 at the o- to h-LiBH4 phase transition.
|
|
| 9. |
- Gloster, Tracey M., et al.
(författare)
-
Characterization and three-dimensional structures of two distinct bacterial xyloglucanases from families GH5 and GH12
- 2007
-
Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 282:26, s. 19177-19189
-
Tidskriftsartikel (refereegranskat)abstract
- The plant cell wall is a complex material in which the cellulose microfibrils are embedded within a mesh of other polysaccharides, some of which are loosely termed hemicellulose. One such hemicellulose is xyloglucan, which displays a beta-1,4-linked D-glucose backbone substituted with xylose, galactose, and occasionally fucose moieties. Both xyloglucan and the enzymes responsible for its modification and degradation are finding increasing prominence, reflecting both the drive for enzymatic biomass conversion, their role in detergent applications, and the utility of modified xyloglucans for cellulose fiber modification. Here we present the enzymatic characterization and three-dimensional structures in ligand free and xyloglucan- oligosaccharide complexed forms of two distinct xyloglucanases from glycoside hydrolase families GH5 and GH12. The enzymes, Paenibacillus pabuli XG5 and Bacillus licheniformis XG12, both display open active center grooves grafted upon their respective (beta/alpha)(8) and beta-jelly roll folds, in which the side chain decorations of xyloglucan may be accommodated. For the beta-jelly roll enzyme topology of GH12, binding of xylosyl and pendant galactosyl moieties is tolerated, but the enzymeis similarly competent in the degradation of unbranched glucans. In the case of the (beta/alpha)(8) GH5 enzyme, kinetically productive interactions are made with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides. The differential strategies for the accommodation of the side chains of xyloglucan presumably facilitate the action of these microbial hydrolases in milieus where diverse and differently substituted substrates may be encountered.
|
|
