| 1. |
- Cruz, Jose Almeida, et al.
(författare)
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RNA-Puzzles : A CASP-like evaluation of RNA three-dimensional structure prediction
- 2012
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Ingår i: RNA. - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 18:4, s. 610-625
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Tidskriftsartikel (refereegranskat)abstract
- We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises.
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| 2. |
- Feng, Lili, et al.
(författare)
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ATR-FTIR for determining optimal cooling curves for batch crystallization of succinic acid
- 2002
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Ingår i: Crystal Growth & Design. - : American Chemical Society (ACS). - 1528-7483 .- 1528-7505. ; 2:5, s. 449-452
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Tidskriftsartikel (refereegranskat)abstract
- The temperature profile applied during batch cooling crystallization affects the supersaturation level, which in turn affects the crystal size distribution. It is possible, in principle, to calculate the optimal cooling profile; however, the nucleation and growth kinetics are rarely known to the degree of accuracy necessary for this calculation. The current study demonstrates an alternative approach to determination of the optimal cooling profile without any prior knowledge of kinetic data or subsequent modeling. An attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectrometer was used to monitor the supersaturation level during batch cooling crystallization. The ATR-FTIR was interfaced to a LABMAX automatic reactor system that was used in a feedback mode to control the cooling rate so that the supersaturation level remained close to the solubility throughout the cooling process. The resulting temperature profile corresponds to the optimal operating conditions for the maximum in the mean crystal size.
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| 3. |
- Li, Wanxin, et al.
(författare)
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Exploring the Complex Relationship between Gut Microbiota and Risk of Colorectal Neoplasia Using Bidirectional Mendelian Randomization Analysis
- 2023
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association For Cancer Research (AACR). - 1055-9965 .- 1538-7755. ; 32:6, s. 809-817
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Tidskriftsartikel (refereegranskat)abstract
- Background: Human gut microbiome has complex relation-ships with the host, contributing to metabolism, immunity, and carcinogenesis.Methods: Summary-level data for gut microbiota and metabo-lites were obtained from MiBioGen, FINRISK and human meta-bolome consortia. Summary-level data for colorectal cancer were derived from a genome-wide association study meta-analysis. In forward Mendelian randomization (MR), we employed genetic instrumental variables (IV) for 24 gut microbiota taxa and six bacterial metabolites to examine their causal relationship with colorectal cancer. We also used a lenient threshold for nine apriori gut microbiota taxa as secondary analyses. In reverse MR, we explored association between genetic liability to colorectal neoplasia and abundance of microbiota studied above using 95, 19, and 7 IVs for colorectal cancer, adenoma, and polyps, respectively.Results: Forward MR did not find evidence indicating causal relationship between any of the gut microbiota taxa or six bacterial metabolites tested and colorectal cancer risk. However, reverse MR supported genetic liability to colorectal adenomas was causally related with increased abundance of two taxa: Gammaproteobacteria (b = 0.027, which represents a 0.027 increase in log-transformed relative abundance values of Gam-maproteobacteria for per one-unit increase in log OR of adenoma risk; P = 7.06x10-8), Enterobacteriaceae (b = 0.023, P = 1.29x10-5).Conclusions: We find genetic liability to colorectal neoplasia may be associated with abundance of certain microbiota taxa. It is more likely that subset of colorectal cancer genetic liability variants changes gut biology by influencing both gut microbiota and colo-rectal cancer risk.Impact: This study highlights the need of future complemen-tary studies to explore causal mechanisms linking both host genetic variation with gut microbiome and colorectal cancer susceptibility.
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| 4. |
- Sigurdsson, Snaevar, et al.
(författare)
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Comprehensive evaluation of the genetic variants of interferon regulatory factor 5 (IRF5) reveals a novel 5 bp length polymorphism as strong risk factor for systemic lupus erythematosus
- 2008
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 17:6, s. 872-881
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Tidskriftsartikel (refereegranskat)abstract
- We analyzed a comprehensive set of single-nucleotide polymorphisms (SNPs) and length polymorphisms in the interferon regulatory factor 5 (IRF5) gene for their association with the autoimmune disease systemic lupus erythematosus (SLE) in 485 Swedish patients and 563 controls. We found 16 SNPs and two length polymorphisms that display association with SLE (P < 0.0005, OR > 1.4). Using a Bayesian model selection and averaging approach we identified parsimonious models with exactly two variants of IRF5 that are independently associated with SLE. The variants of IRF5 with the highest posterior probabilities (1.00 and 0.71, respectively) of being causal in SLE are a SNP (rs10488631) located 3' of IRF5, and a novel CGGGG insertion-deletion (indel) polymorphism located 64 bp upstream of the first untranslated exon (exon 1A) of IRF5. The CGGGG indel explains the association signal from multiple SNPs in the IRF5 gene, including rs2004640, rs10954213 and rs729302 previously considered to be causal variants in SLE. The CGGGG indel contains three or four repeats of the sequence CGGGG with the longer allele containing an additional SP1 binding site as the risk allele for SLE. Using electrophoretic mobility shift assays we show increased binding of protein to the risk allele of the CGGGG indel and using a minigene reporter assay we show increased expression of IRF5 mRNA from a promoter containing this allele. Increased expression of IRF5 protein was observed in peripheral blood mononuclear cells from SLE patients carrying the risk allele of the CGGGG indel. We have found that the same IRF5 allele also confers risk for inflammatory bowel diseases and multiple sclerosis, suggesting a general role for IRF5 in autoimmune diseases.
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| 5. |
- Song, Jiali, et al.
(författare)
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Solid additive engineering enables high-efficiency and eco-friendly all-polymer solar cells
- 2022
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Ingår i: Matter. - : ELSEVIER. - 2590-2393 .- 2590-2385. ; 5:11, s. 4047-4059
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Tidskriftsartikel (refereegranskat)abstract
- Currently, morphology optimization of all-polymer solar cells (all-PSCs) strongly depends on the use of solvent additives, which are usually highly toxic and harmful to the environment and human health. Here, we report a green and volatile solid additive, 2-methoxynaphthalene (2-MN). It was found that the incorporation of 2-MN into a PM6:PY-DT blend can effectively manipulate the aggregations of PM6 and PY-DT during film depositing and thermal annealing processes and results in highly ordered molecular packing and favorable phase-separated morphology. Consequently, a re-cord-high efficiency of 17.32% is achieved for the PM6:PY-DT de-vice. Moreover, 2-MN-processed all-PSCs were fabricated by using non-halogenated solvent. High efficiencies of 17.03% and 16.67% are obtained for all-PSCs fabricated under nitrogen atmosphere and ambient conditions, respectively. Our work shows that the utili-zation of 2-MN as a green and solid additive is a simple and feasible strategy to optimize the morphology and sheds new light on eco-friendly fabrication and application of all-PSCs.
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| 6. |
- Sun, Tao, et al.
(författare)
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Empirical evidence that manganese enrichment accelerates decomposition
- 2021
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Ingår i: Agriculture, Ecosystems & Environment. Applied Soil Ecology. - : Elsevier. - 0929-1393 .- 1873-0272. ; 168
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Tidskriftsartikel (refereegranskat)abstract
- Our understanding of the controls regulating the rate of litter decomposition is important for improving confidence in the parameterization of carbon cycle–climate feedbacks. Traditional conceptual models rely primarily on climate and lignin/N ratios as the main regulators of decomposition. Here we studied the effects of manganese (Mn) addition on long-term decomposition across 18 substrates in a laboratory incubation. Mn addition remarkably promoted later stage of decomposition, resulting into a smaller fraction of slowly decomposing litter. This dynamic is closely associated with the changes of activities of manganese peroxidase, an important enzyme with greater capacity for lignin degradation. Our findings suggest the necessity of incorporating the interaction of Mn and decomposition into biogeochemical models.
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| 7. |
- 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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| 8. |
- Wang, Hui-Xin, et al.
(författare)
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Late Life Leisure Activities and Risk of Cognitive Decline
- 2013
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Ingår i: The journals of gerontology. Series A, Biological sciences and medical sciences. - : Oxford University Press (OUP). - 1079-5006 .- 1758-535X. ; 68:2, s. 205-213
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Tidskriftsartikel (refereegranskat)abstract
- Background. Studies concerning the effect of different types of leisure activities on various cognitive domains are limited. This study tests the hypothesis that mental, physical, and social activities have a domain-specific protection against cognitive decline. Methods. A cohort of a geographically defined population in China was examined in 2003-2005 and followed for an average of 2.4 years. Leisure activities were assessed in 1,463 adults aged 65 years and older without cognitive or physical impairment at baseline, and their cognitive performances were tested at baseline and follow-up examinations. Results. High level of mental activity was related to less decline in global cognition (beta = -.23, p < .01), language (beta = -.11, p < .05), and executive function (beta = -.13, p < .05) in ANCOVA models adjusting for age, gender, education, history of stroke, body mass index, Apolipoprotein E genotype, and baseline cognition. High level of physical activity was related to less decline in episodic memory (beta = -.08, p < .05) and language (beta = -.15, p < .01). High level of social activity was associated with less decline in global cognition (beta = -.11, p < .05). Further, a dose-response pattern was observed: although participants who did not engage in any of the three activities experienced a significant global cognitive decline, those who engaged in any one of the activities maintained their cognition, and those who engaged in two or three activities improved their cognition. The same pattern was observed in men and in women. Conclusions. Leisure activities in old age may protect against cognitive decline for both women and men, and different types of activities seem to benefit different cognitive domains.
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| 9. |
- Wei, Jiang, et al.
(författare)
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Estrogen upregulates hepatic apolipoprotein M expression via the estrogen receptor
- 2011
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Ingår i: Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids. - : Elsevier BV. - 1388-1981. ; 1811:12, s. 1146-1151
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Tidskriftsartikel (refereegranskat)abstract
- Apolipoprotein M (apoM) is present predominantly in high-density lipoprotein (HDL) in human plasma, thus possibly involved in the regulation of HDL metabolism and the process of atherosclerosis. Although estrogen replacement therapy increases serum levels of apoAl and HDL, it does not seem to reduce the cardiovascular risk in postmenopausal women. Therefore, we investigated the effects of estrogen on apoM expression in vitro and in vivo. HepG2 cells were incubated with different concentrations of estrogen with or without the estrogen receptor antagonist, fulvestrant, and apoM expression in the cells was determined. Hepatic apoM expression and serum levels of apoM were also determined in normal and in ovariectomized rats treated with either placebo or estradiol benzoate, using sham operated rats as controls. Estrogen significantly increased mRNA levels of apoM and apoAl in HepG2 cell cultures in a dose- and time-dependent manner; the upregulation of both apolipoproteins was fully abolished by addition of estrogen receptor antagonist In normal rats, estrogen treatment led to an increase in plasma lipid levels including HDL cholesterol, a marked upregulation of apoM mRNA and a significant increase in serum levels of apoM. The same pattern of regulation was found in ovariectomized rats treated with estrogen. Thus, estrogen upregulates apoM expression both in vivo and in vitro by mechanism(s) involving the estrogen receptor. (C) 2011 Elsevier B.V. All rights reserved.
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| 10. |
- Xiong, Weixi, et al.
(författare)
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Circulatory microRNA 23a and microRNA 23b and polycystic ovary syndrome (PCOS): the effects of body mass index and sex hormones in an Eastern Han Chinese population.
- 2017
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Ingår i: Journal of ovarian research. - : Springer Science and Business Media LLC. - 1757-2215. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- MicroRNAs (miRNAs) regulate the expression of genes involved in various cellular functions related to metabolism, inflammation, and reproduction. This study evaluated the effects of sex hormones and obesity on the expression of circulating miR-23a and miR-23b in women with polycystic ovary syndrome (PCOS) and healthy women.Serum sex hormones concentrations and body mass index (BMI) were measured in 18 women with PCOS and in 30 healthy women from the East China area and these measurements were correlated with serum miR-23a/b levels. The effect of miR-23a and miR-23b risk factors on occurrence of PCOS and predisposing factors of PCOS on these miRNA expressions were evaluated.The expressions of miR-23a/b were significantly lower in the women with PCOS than the normal women, and the expression levels of miR-23a/b were positively correlated with each other in the normal women (p=0.001) but not in the women with PCOS (p>0.05). In the women with PCOS, miR-23a was positively correlated with BMI (p=0.03). However, no correlations were found between the levels of miR-23a/b and the sex hormones in the normal and PCOS women. On the other hand, without considering the presence or absence of PCOS, increase in BMI had a positive effect on the levels of circulating miR-23b; while testosterone had negative effects on the levels of circulating miR-23a. Furthermore, the likelihood of women with PCOS decreased by 0.01-fold for every 1 fold increase of miR-23a expression.Both reduced levels and discordance between the expressions of miR-23a/b were observed in the women with PCOS and miR-23a/b were affected from testosterone and BMI, reversely. Therefore, miR-23a alteration in contrast with miR-23b is a better indicator for evaluation of PCOS than the miR-23b.
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