| 1. |
- Xia, Yi Han, et al.
(author)
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Multi-Functional Desaturases in Two Spodoptera Moths with ∆11 and ∆12 Desaturation Activities
- 2019
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In: Journal of Chemical Ecology. - : Springer Science and Business Media LLC. - 0098-0331 .- 1573-1561. ; 45:4, s. 378-387
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Journal article (peer-reviewed)abstract
- The beet armyworm, Spodoptera exigua, uses (Z,E)-9,12-tetradecadienyl acetate as the major component of its sex pheromone. Previous isotope-labeling experiments demonstrated an unusual ∆12 desaturase activity involved in the biosynthesis of this compound; however, the putative ∆12 desaturase gene has not been reported to date. In the present study, we confirmed this ∆12 desaturation pathway by in vivo labeling experiments, and characterized candidate desaturase genes in a yeast heterologous expression system. We demonstrated that a pheromone gland-specific desaturase, SexiDes5, uses palmitic acid and the subsequently chain-shortened product (Z)-9-tetradecenoic acid as substrates to produce (Z)-11-hexadecenoic and (Z,E)-9,12-tetradecadienoic acids, respectively. In addition, the homologous desaturase SlitDes5 from the congeneric Spodoptera litura had analogous functions.
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| 2. |
- Ding, Huaiyi, et al.
(author)
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Maximizing Integrated Optical and Electrical Properties of a Single ZnO Nanowire through Native Interfacial Doping
- 2014
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In: Advanced Materials. - : Wiley. - 0935-9648 .- 1521-4095. ; 26:19, s. 3035-3041
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Journal article (peer-reviewed)abstract
- A native interfacial doping layer introduced in core-shell type ZnO nanowires by a simple vapor phase re-growth procedure endows the produced nanowires with both excellent electrical and optical performances compared to conventional homogeneous ZnO nanowires. The unique Zn-rich interfacial structure in the core-shell nanowires plays a crucial role in the outstanding performances.
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| 3. |
- Ding, Shaozhen, et al.
(author)
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novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
- 2020
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:W1, s. W477-W487
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Journal article (peer-reviewed)abstract
- To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/.
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| 4. |
- Han, Mengying, et al.
(author)
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ChemHub: a knowledgebase of functional chemicals for synthetic biology studies
- 2021
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In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 37:22, s. 4275-4276
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Journal article (peer-reviewed)abstract
- The field of synthetic biology lacks a comprehensive knowledgebase for selecting synthetic target molecules according to their functions, economic applications and known biosynthetic pathways. We implemented ChemHub, a knowledgebase containing >90 000 chemicals and their functions, along with related biosynthesis information for these chemicals that was manually extracted from >600 000 published studies by more than 100 people over the past 10 years.
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| 5. |
- Jacobs, Kevin B, et al.
(author)
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Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
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In: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
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Journal article (peer-reviewed)abstract
- In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.
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| 6. |
- Ji, Yanan, et al.
(author)
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Cascade photon upconversion amplification for selective multispectral narrow-band near-infrared photodetection
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Other publication (other academic/artistic)abstract
- Facing the fact that selective detection of multiple narrow spectral bands in the near-infrared (NIR) region still poses a fundamental challenge, we have, in this work, developed NIR photodetectors (PDs) using photon upconversion nanocrystals (UCNCs) combined with perovskite films. In order to conquer the relatively high pumping threshold of UCNCs, we designed a novel cascade amplification strategy for upconversion luminescence (UCL) through cascading the superlensing effect of dielectric microlens arrays and the plasmonic effect of gold nanorods, which readily leads to a UCL enhancement by more than four orders of magnitude under weak light irradiation. By accommodating multiple optical active lanthanide ions in a core-shell-shell hierarchical architecture, the developed PDs on top can detect three well-separated narrow bands in the NIR region, i.e., 808, 980, and 1540 nm, respectively. Due to the large UCL enhancement, the obtained PDs demonstrate extremely high responsivity of 30.73, 23.15, 12.20 A/W and detectivity of 5.36, 3.45, 1.91x10^11 Jones for the 808, 980, and 1540 nm light detection, respectively, together with short response times in the range of 80-120 ms. Moreover, we demonstrate for the first time that the response to the excitation modulation frequency of a PD can be employed to discriminate the incident light wavelength. We believe that our work provides a novel insight for developing NIR PDs, and that it can spur the development of other applications using upconversion nanotechnology.
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| 7. |
- Ji, Yanan, et al.
(author)
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Huge upconversion luminescence enhancement by a cascade optical field modulation strategy facilitating selective multispectral narrow-band near-infrared photodetection
- 2020
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In: Light. - : SPRINGERNATURE. - 2095-5545 .- 2047-7538. ; 9:1
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Journal article (peer-reviewed)abstract
- Since selective detection of multiple narrow spectral bands in the near-infrared (NIR) region still poses a fundamental challenge, we have, in this work, developed NIR photodetectors (PDs) using photon upconversion nanocrystals (UCNCs) combined with perovskite films. To conquer the relatively high pumping threshold of UCNCs, we designed a novel cascade optical field modulation strategy to boost upconversion luminescence (UCL) by cascading the superlensing effect of dielectric microlens arrays and the plasmonic effect of gold nanorods, which readily leads to a UCL enhancement by more than four orders of magnitude under weak light irradiation. By accommodating multiple optically active lanthanide ions in a core-shell-shell hierarchical architecture, developed PDs on top of this structure can detect three well-separated narrow bands in the NIR region, i.e., those centered at 808, 980, and 1540 nm. Due to the large UCL enhancement, the obtained PDs demonstrate extremely high responsivities of 30.73, 23.15, and 12.20 A W-1 and detectivities of 5.36, 3.45, and 1.91 x 10(11) Jones for 808, 980, and 1540 nm light detection, respectively, together with short response times in the range of 80-120 ms. Moreover, we demonstrate for the first time that the response to the excitation modulation frequency of a PD can be employed to discriminate the incident light wavelength. We believe that our work provides novel insight for developing NIR PDs and that it can spur the development of other applications using upconversion nanotechnology. Cascade amplified upconversion luminescence: Applied in narrow band NIR photodetection Selective detection of multiple narrow spectral bands in the near-infrared (NIR) region is still a challenge. Recently, Hongwei Song and Wen Xu at Jilin University/China, Haichun Liu at KTH Royal Institute of Technology/Sweden, and their co-workers have successfully fabricated a novel multiple NIR bands photo-detectors (PDs) by combining multiple-excitation-bands core-shell upconversion nanocrystals (UCNCs) with MAPbI(3) perovskite photoelectric conversion layer. Through a cascade optical field modulation strategy, a combination of microlenses and gold plasmon nanocrystals, the emission intensity of the UCNCs and the photoelectric signal of the PDs can be enhanced four orders of magnitude. Moreover, the excitation frequency of the PD has been employed to discriminate the wavelength of incident light for the first time. This work provides a novel insight for developing multiple bands NIR PDs, and for applications of upconversion nanotechnology.
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| 8. |
- Lyon, Helen N., et al.
(author)
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The association of a SNP upstream of INSIG2 with body mass index is reproduced in several but not all cohorts
- 2007
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In: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 3:4
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Journal article (peer-reviewed)abstract
- A SNP upstream of the INSIG2 gene, rs7566605, was recently found to be associated with obesity as measured by body mass index (BMI) by Herbert and colleagues. The association between increased BMI and homozygosity for the minor allele was first observed in data from a genome-wide association scan of 86,604 SNPs in 923 related individuals from the Framingham Heart Study offspring cohort. The association was reproduced in four additional cohorts, but was not seen in a fifth cohort. To further assess the general reproducibility of this association, we genotyped rs7566605 in nine large cohorts from eight populations across multiple ethnicities (total n = 16,969). We tested this variant for association with BMI in each sample under a recessive model using family-based, population-based, and case-control designs. We observed a significant (p < 0.05) association in five cohorts but saw no association in three other cohorts. There was variability in the strength of association evidence across examination cycles in longitudinal data from unrelated individuals in the Framingham Heart Study Offspring cohort. A combined analysis revealed significant independent validation of this association in both unrelated (p = 0.046) and family-based (p = 0.004) samples. The estimated risk conferred by this allele is small, and could easily be masked by small sample size, population stratification, or other confounders. These validation studies suggest that the original association is less likely to be spurious, but the failure to observe an association in every data set suggests that the effect of SNP rs7566605 on BMI may be heterogeneous across population samples.
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| 9. |
- Machiela, Mitchell J., et al.
(author)
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Characterization of Large Structural Genetic Mosaicism in Human Autosomes
- 2015
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In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 96:3, s. 487-497
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Journal article (peer-reviewed)abstract
- Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.
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| 10. |
- Machiela, Mitchell J, et al.
(author)
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Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
- 2016
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In: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 7
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Journal article (peer-reviewed)abstract
- To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
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