| 1. |
- Kanoni, Stavroula, et al.
(författare)
-
Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
-
Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
-
Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
|
|
| 2. |
- Mahajan, Anubha, et al.
(författare)
-
Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation
- 2022
-
Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 54:5, s. 560-572
-
Tidskriftsartikel (refereegranskat)abstract
- We assembled an ancestrally diverse collection of genome-wide association studies (GWAS) of type 2 diabetes (T2D) in 180,834 affected individuals and 1,159,055 controls (48.9% non-European descent) through the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. Multi-ancestry GWAS meta-analysis identified 237 loci attaining stringent genome-wide significance (P < 5 x 10(-9)), which were delineated to 338 distinct association signals. Fine-mapping of these signals was enhanced by the increased sample size and expanded population diversity of the multi-ancestry meta-analysis, which localized 54.4% of T2D associations to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying the foundations for functional investigations. Multi-ancestry genetic risk scores enhanced transferability of T2D prediction across diverse populations. Our study provides a step toward more effective clinical translation of T2D GWAS to improve global health for all, irrespective of genetic background. Genome-wide association and fine-mapping analyses in ancestrally diverse populations implicate candidate causal genes and mechanisms underlying type 2 diabetes. Trans-ancestry genetic risk scores enhance transferability across populations.
|
|
| 3. |
- Takeuchi, Fumihiko, et al.
(författare)
-
Interethnic analyses of blood pressure loci in populations of East Asian and European descent
- 2018
-
Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 9:1
-
Tidskriftsartikel (refereegranskat)abstract
- Blood pressure (BP) is a major risk factor for cardiovascular disease and more than 200 genetic loci associated with BP are known. Here, we perform a multi-stage genome-wide association study for BP (max N = 289,038) principally in East Asians and meta-analysis in East Asians and Europeans. We report 19 new genetic loci and ancestry-specific BP variants, conforming to a common ancestry-specific variant association model. At 10 unique loci, distinct non-rare ancestry-specific variants colocalize within the same linkage disequilibrium block despite the significantly discordant effects for the proxy shared variants between the ethnic groups. The genome-wide transethnic correlation of causal-variant effect-sizes is 0.898 and 0.851 for systolic and diastolic BP, respectively. Some of the ancestry-specific association signals are also influenced by a selective sweep. Our results provide new evidence for the role of common ancestry-specific variants and natural selection in ethnic differences in complex traits such as BP.
|
|
| 4. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 5. |
- Callaway, EM, et al.
(författare)
-
A multimodal cell census and atlas of the mammalian primary motor cortex
- 2021
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
-
Tidskriftsartikel (refereegranskat)abstract
- Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
|
|
| 6. |
- Chen, Chi-Kuang, et al.
(författare)
-
Greenhouse gas management model - a triple cause-effect logic
- 2016
-
Ingår i: International Journal of Quality and Service Sciences. - : EMERALD GROUP PUBLISHING LTD. - 1756-669X .- 1756-6703. ; 8:3, s. 412-427
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose - The purpose of this paper is to develop a greenhouse gas (GHG) management model for mitigating GHG emission. GHG emission by way of human activities is causing catastrophic effects on the natural environment in the form of climate change and global warming. GHG management of different products, bodies and processes is going on worldwide, expressed through carbon footprints by using product life cycle assessment (LCA). LCA is a useful approach, but it only looks at the micro level of cause-effect scenarios rather than the macro level cause-effect scenarios of GHG emission. Therefore, a system to scrutinize underlined assumptions and values of such policies/strategies is an urgent necessity. Design/methodology/approach - This paper uses the double-loop learning concept, which was proposed by Argyris in 1976, to develop a triple cause-effect model for the management of GHG emission. The proposed model has a knowledge system that introduces the learning loop of GHG emission and environmental impact management. Findings - A case study is conducted to demonstrate how the proposed triple cause-effect model is operationalized. The ideas and benefits of the proposed model are further discussed. Originality/value - Atriple cause-effect model for the measurement and analysis of GHG emission is proposed in this paper to complement GHG management by using only product LCA. This paper seeks to show thatGHGmanagement should look at not only a single tree (product LCA approach) but also the whole forest (the proposed model).
|
|
| 7. |
- Feng, Ruizhi, et al.
(författare)
-
Mutations in TUBB8 and Human Oocyte Meiotic Arrest.
- 2016
-
Ingår i: The New England journal of medicine. - 1533-4406. ; 374:3, s. 223-232
-
Tidskriftsartikel (refereegranskat)abstract
- Background Human reproduction depends on the fusion of a mature oocyte with a sperm cell to form a fertilized egg. The genetic events that lead to the arrest of human oocyte maturation are unknown. Methods We sequenced the exomes of five members of a four-generation family, three of whom had infertility due to oocyte meiosis I arrest. We performed Sanger sequencing of a candidate gene, TUBB8, in DNA samples from these members, additional family members, and members of 23 other affected families. The expression of TUBB8 and all other β-tubulin isotypes was assessed in human oocytes, early embryos, sperm cells, and several somatic tissues by means of a quantitative reverse-transcriptase-polymerase-chain-reaction assay. We evaluated the effect of the TUBB8 mutations on the assembly of the heterodimer consisting of one α-tubulin polypeptide and one β-tubulin polypeptide (α/β-tubulin heterodimer) in vitro, on microtubule architecture in HeLa cells, on microtubule dynamics in yeast cells, and on spindle assembly in mouse and human oocytes. Results We identified seven mutations in the primate-specific gene TUBB8 that were responsible for oocyte meiosis I arrest in 7 of the 24 families. TUBB8 expression is unique to oocytes and the early embryo, in which this gene accounts for almost all the expressed β-tubulin. The mutations affect chaperone-dependent folding and assembly of the α/β-tubulin heterodimer, disrupt microtubule behavior on expression in cultured cells, alter microtubule dynamics in vivo, and cause catastrophic spindle-assembly defects and maturation arrest on expression in mouse and human oocytes. Conclusions TUBB8 mutations have dominant-negative effects that disrupt microtubule behavior and oocyte meiotic spindle assembly and maturation, causing female infertility. (Funded by the National Basic Research Program of China and others.).
|
|
| 8. |
- Haycock, Philip C., et al.
(författare)
-
Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases A Mendelian Randomization Study
- 2017
-
Ingår i: JAMA Oncology. - : American Medical Association. - 2374-2437 .- 2374-2445. ; 3:5, s. 636-651
-
Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE: The causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. OBJECTIVE: To conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases. DATA SOURCES: Genomewide association studies (GWAS) published up to January 15, 2015. STUDY SELECTION: GWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available. DATA EXTRACTION AND SYNTHESIS: Summary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population. MAIN OUTCOMES AND MEASURES: Odds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation. RESULTS: Summary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [ 95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [ 95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [ 95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [ 95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [ 95% CI, 0.05-0.15]). CONCLUSIONS AND RELEVANCE: It is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
|
|
| 9. |
|
|
| 10. |
- Hou, Meijun, et al.
(författare)
-
Human dopaminergic system in the exercise-cognition link
- 2024
-
Ingår i: Trends in Molecular Medicine. - : Elsevier. - 1471-4914 .- 1471-499X.
-
Tidskriftsartikel (refereegranskat)abstract
- While the dopaminergic system is important for cognitive processes, it is also sensitive to the influence of physical activity (PA). We summarize current evidence on whether PA-related changes in the human dopaminergic system are associated with alterations in cognitive performance, discuss recent advances, and highlight challenges and opportunities for future research.
|
|
| 11. |
- Koller, Thaddaeus J., et al.
(författare)
-
Simple Molecules under High-Pressure and High-Temperature Conditions: Synthesis and Characterization of α- and β-C(NH)2 with Fully sp3-Hybridized Carbon
- 2024
-
Ingår i: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773.
-
Tidskriftsartikel (refereegranskat)abstract
- The elements hydrogen, carbon, and nitrogen are among the most abundant in the solar system. Still, little is known about the ternary compounds these elements can form under the high-pressure and high-temperature conditions found in the outer planets' interiors. These materials are also of significant research interest since they are predicted to feature many desirable properties such as high thermal conductivity and hardness due to strong covalent bonding networks. In this study, the high-pressure high-temperature reaction behavior of malononitrile H2C(CN)(2), dicyandiamide (H2N)(2)C=NCN, and melamine (C3N3)(NH2)(3) was investigated in laser-heated diamond anvil cells. Two previously unknown compounds, namely alpha-C(NH)(2) and beta-C(NH)(2), have been synthesized and found to have fully sp(3)-hybridized carbon atoms. alpha-C(NH)(2) crystallizes in a distorted beta-cristobalite structure, while beta-C(NH)(2) is built from previously unknown imide-bridged 2,4,6,8,9,10-hexaazaadamantane units, which form two independent interpenetrating diamond-like networks. Their stability domains and compressibility were studied, for which supporting density functional theory calculations were performed.
|
|
| 12. |
|
|
| 13. |
- Laisk, Triin, et al.
(författare)
-
The genetic architecture of sporadic and multiple consecutive miscarriage.
- 2020
-
Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Miscarriage is a common, complex trait affecting ~15% of clinically confirmed pregnancies. Here we present the results of large-scale genetic association analyses with 69,054 cases from five different ancestries for sporadic miscarriage, 750 cases of European ancestry for multiple (≥3) consecutive miscarriage, and up to 359,469 female controls. We identify one genome-wide significant association (rs146350366, minor allele frequency (MAF) 1.2%, P=3.2 × 10-8, odds ratio (OR)=1.4) for sporadic miscarriage in our European ancestry meta-analysis and three genome-wide significant associations for multiple consecutive miscarriage (rs7859844, MAF=6.4%, P=1.3 × 10-8, OR=1.7; rs143445068, MAF=0.8%, P=5.2 × 10-9, OR=3.4; rs183453668, MAF=0.5%, P=2.8 × 10-8, OR=3.8). We further investigate the genetic architecture of miscarriage with biobank-scale Mendelian randomization, heritability, and genetic correlation analyses. Our results show that miscarriage etiopathogenesis is partly driven by genetic variation potentially related to placental biology, and illustrate the utility of large-scale biobank data for understanding this pregnancy complication.
|
|
| 14. |
- Lee, Chunsik, et al.
(författare)
-
VEGF-B prevents excessive angiogenesis by inhibiting FGF2/FGFR1 pathway
- 2023
-
Ingår i: SIGNAL TRANSDUCTION AND TARGETED THERAPY. - : SPRINGERNATURE. - 2095-9907 .- 2059-3635. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- Although VEGF-B was discovered as a VEGF-A homolog a long time ago, the angiogenic effect of VEGF-B remains poorly understood with limited and diverse findings from different groups. Notwithstanding, drugs that inhibit VEGF-B together with other VEGF family members are being used to treat patients with various neovascular diseases. It is therefore critical to have a better understanding of the angiogenic effect of VEGF-B and the underlying mechanisms. Using comprehensive in vitro and in vivo methods and models, we reveal here for the first time an unexpected and surprising function of VEGF-B as an endogenous inhibitor of angiogenesis by inhibiting the FGF2/FGFR1 pathway when the latter is abundantly expressed. Mechanistically, we unveil that VEGF-B binds to FGFR1, induces FGFR1/VEGFR1 complex formation, and suppresses FGF2-induced Erk activation, and inhibits FGF2-driven angiogenesis and tumor growth. Our work uncovers a previously unrecognized novel function of VEGF-B in tethering the FGF2/FGFR1 pathway. Given the anti-angiogenic nature of VEGF-B under conditions of high FGF2/FGFR1 levels, caution is warranted when modulating VEGF-B activity to treat neovascular diseases.
|
|
| 15. |
- Song, Hosub, et al.
(författare)
-
A Small Peak in the Swarm-LP Plasma Density Data at the Dayside Dip Equator
- 2022
-
Ingår i: Journal of Geophysical Research - Space Physics. - : American Geophysical Union (AGU). - 2169-9380 .- 2169-9402. ; 127:7
-
Tidskriftsartikel (refereegranskat)abstract
- In this paper, we statistically investigate an artifact in Langmuir Probe (LP) observations of Swarm satellites. A small peak of electron density (N-e) is frequently found in the Swarm data around the dayside dip equator. On the contrary, they appear in neither the Total Electron Content data of the Swarm/Global Positioning System Receivers nor COSMIC-2 in-situ measurements at similar altitudes but with low orbit inclination. Arguably, this peak does not represent natural ionospheric irregularities but is likely to result from artifacts. The phenomena are found regardless of the season, solar activity, and the velocity direction of the satellite (ascending and descending). They predominantly occur when the magnetic declination is close to zero, that is, when the Swarm ram direction and the Earth's magnetic field are aligned under sunlight. Hence, we attribute the phenomenon to intensified secondary electrons escape when the geomagnetic field lines are normal to conducting surfaces that emit secondary electrons. Since the magnitude of the artifact is only a few percent of the large-scale background, it does not have a serious impact on the value of the Swarm/LP data in scientific research. Nevertheless, future efforts to determine the exact cause of the artifacts will contribute to improving the reliability and quality of plasma density and temperature measured by Swarm/LP.
|
|
| 16. |
- Zhang, Daquan, et al.
(författare)
-
Large-scale planar and spherical light-emitting diodes based on arrays of perovskite quantum wires
- 2022
-
Ingår i: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 16:4, s. 284-290
-
Tidskriftsartikel (refereegranskat)abstract
- Halide perovskites are enticing candidates for highly efficient planar light-emitting diodes (LEDs) with commercial potential in displays and lighting. However, it remains a challenge for conventional solution fabrication processes to fabricate large-scale or non-planar LEDs due to the non-uniformity of perovskite films in conjunction with material stability issues. Here large-area highly uniform arrays of crystalline perovskite quantum wires are grown with emission spectra covering the whole visible range. Photoluminescence quantum yield of up to 92% and 5,644 hours as the time for photoluminescence to degrade down to its 50% of the initial value under ambient conditions are achieved for MAPbBr3 quantum wires. LEDs based on these quantum wires on rigid and flexible planar substrates are fabricated up to a four-inch wafer size and also unique three-dimensional spherical LEDs with outstanding uniformity are reported. The results suggest that the approach developed here can be generalized to other unconventional three-dimensional LEDs in the future.
|
|
