| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Beijer, Kristina, et al.
(författare)
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Effluent from drug manufacturing affects cytochrome P450 1 regulation and function in fish
- 2013
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 90:3, s. 1149-1157
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Tidskriftsartikel (refereegranskat)abstract
- We have previously reported very high concentrations of pharmaceuticals in the effluent from a treatment plant receiving wastewater from about 90 bulk drug manufacturers near Hyderabad, India. The main objective of the present study was to examine how high dilutions of this effluent affect mRNA expression of cytochrome P450 (CYP) 1 family genes and ethoxyresorufin O-deethylase (EROD) activity in exposed wildlife, using the three-spined stickleback (Gasterosteus aculeatus) as a model. In gill filaments exposed to diluted effluent ex vivo, EROD activity was strongly inhibited in a concentration-dependent manner. In a subsequent in vivo study, groups of fish were exposed (24. h) to three concentrations of effluent, 0.8%, 1.6% or 3.2%. In this experiment, EROD in gills was induced 27-, 52- or 60-fold, respectively. Accordingly, CYP1A mRNA was markedly up-regulated in gill, liver and brain of fish exposed to all three effluent concentrations. Expression of mRNA for CYP1B1 and CYP1C1 was induced in gills at all concentrations while effects on these genes in liver and brain were weak or absent. The results of a time course study suggested that most CYP1-inducing substances in the effluent were readily metabolised or excreted, because the induced EROD activity and mRNA expression decreased when the fish were transferred to clean water. Considering that CYP1 enzymes play important roles in biotransformation of endogenous and foreign compounds, the observed dual effect of the effluent on CYP1 catalytic activity and mRNA expression suggests that multiple physiological functions could be affected in exposed wildlife.
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| 3. |
- Chen, Kai, et al.
(författare)
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Room-temperature multiferroic properties in NiBi2O4
- 2010
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Ingår i: Europhysics letters. - : European Physical Society. - 0295-5075 .- 1286-4854. ; 89:2
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Tidskriftsartikel (refereegranskat)abstract
- Magnetism and ferroelectricity at room temperature are observed in the NiBi2O4 ceramics. Both the time reversal and the inversion symmetry of the structure (space group F-43m) are broken. The saturation magnetization is 0.028 emu/g and the saturation polarization 2P(s) similar to 4.0 mu C/cm(2). NiBi2O4 also shows other room-temperature multiferroic properties, e. g. the piezoelectric coefficient (d(33)), the polarized dielectric character, the magneto-dielectric response and the magnetoelectric effect. Copyright (C) EPLA, 2010
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| 4. |
- Dai, Tingyang, et al.
(författare)
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Sequential Polymer Precipitation of Core-Shell Microstructured Composites with Giant Permittivity
- 2010
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Ingår i: Macromolecular rapid communications. - : Wiley-VCH Verlag. - 1022-1336 .- 1521-3927. ; 31:5, s. 484-489
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Tidskriftsartikel (refereegranskat)abstract
- Polymeric core shell microstructures have been constructed through a new method, namely sequential precipitation, which is intrinsically a self-assembly and phase separation process. High-quality poly(vinyldene fluoride)-polycarbonate-lithium perchlorate composite films with spherical core shell microstructures have been prepared and determined to consist of conducting cores and insulating shells. Because of the percolation effect, the resulting materials present a dielectric constant as high as 10(4)-10(7) at the threshold.
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| 5. |
- Gao, Kai
(författare)
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Basal and Pollutant-induced Expression of CYP1A, 1B and 1C isoforms in Fish : Implications for Biomonitoring
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Aquatic wildlife are exposed to contaminants in their natural habitats, and toxic pollutants may induce toxicity in sensitive target tissues and cells. There is therefore a need to establish biomarkers to determine exposure to certain classes of contaminants and the subsequent biological responses. In the present work the whole suite of cytochrome P450 1 (CYP1) genes expressed in fish were examined with regard to their inducibility and potential use as biomarkers. Complementary DNA of the CYP1A, 1B and 1C transcripts in rainbow trout and three-spined stickleback were cloned and characterized by quantitative mRNA expression analysis. All CYP1 transcripts could be induced by two selected aryl hydrocarbon receptor (AhR) agoinsts (indigo and PCB 126) in both species, suggesting that all genes were regulated by the AhR. CYP1 mRNA expression profiles induced by PCB 126 and indigo varied over time showing that PCB 126 gave rise to a high and persistent induction in gills and liver while induction by indigo was transient in both organs. The uptake and kinetics of 14C-indigo was studied by autoradiography in rainbow trout. A rapid uptake of 14C-indigo from the water and a subsequent elimination in bile and intestinal contents was observed, explaining the transient CYP1 induction. A high accumulation of 14C-indigo in the gills was completely blocked the CYP1 inhibitor ellipticine, suggesting a CYP1-dependent uptake. High dilutions of a sewage treatment plant effluent containing a complex mixture of pharmaceuticals were investigated. The same water sample both induced CYP1A mRNA expression and inhibited catalytic activity of CYP1A. A field study revealed different induction signatures of the CYP1 genes examined at various locations in Uppsala water environments. As concluded by the temporal and spatial responses obtained, the results of this work suggest that the CYP1 gene panel could be used for biomonitoring of environmental contaminants acting on the CYP system. Further field studies will be required to evaluate this possibility.
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| 6. |
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| 7. |
- Gao, Kai, et al.
(författare)
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Cytochrome P450 1A, 1B, and 1C mRNA induction patterns in three-spined stickleback exposed to a transient and a persistent inducer
- 2011
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Ingår i: Comparative Biochemistry and Physiology - Part C. - : Elsevier BV. - 1532-0456 .- 1878-1659. ; 154:1, s. 42-55
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Tidskriftsartikel (refereegranskat)abstract
- Cytochrome P450 1 (CYP1) mRNA induction patterns in three-spined stickleback (Gasterosteus aculeatus) were explored for use in environmental monitoring of aryl hydrocarbon receptor (AHR) agonists. The cDNAs of stickleback CYP1A, CYP1B1, CYP1C1, and CYP1C2 were cloned and their basal and induced expression patterns were determined in the brain, gill, liver and kidney. Also, their induction time courses were compared after waterborne exposure to a transient (indigo) or a persistent (3,3',4,4',5-pentacholorbiphenyl PCB 126) AHR agonist. The cloned stickleback CYP1s exhibited a high amino acid sequence identity compared with their zebrafish orthologs and their constitutive tissue distribution patterns largely agreed with those reported in other species. PCB 126 (100 nM) induced different CYP1 expression patterns in the four tissues, suggesting tissue-specific regulation. Both indigo (1 nM) and PCB 126 (10 nM) induced a strong CYP1 expression in gills. However, while PCB 126 gave rise to a high and persistent induction in gills and liver, induction by indigo was transient in both organs. The number of putative dioxin response elements found in each CYP1 gene promoter roughly reflected the induction levels of the genes. The high responsiveness of CYP1A,CYP1B1, and CYP1C1 observed in several organs suggests that three-spined stickleback is suitable for monitoring of pollution with AHR agonists.
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| 8. |
- Jacobs, Kevin B, et al.
(författare)
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Detectable clonal mosaicism and its relationship to aging and cancer.
- 2012
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Ingår i: Nature Genetics. - New York : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 44:6, s. 651-658
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Tidskriftsartikel (refereegranskat)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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| 9. |
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| 10. |
- Jönsson, Maria E., et al.
(författare)
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Induction patterns of new CYP1 genes in environmentally exposed rainbow trout
- 2010
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Ingår i: Aquatic Toxicology. - : Elsevier BV. - 0166-445X .- 1879-1514. ; 98:4, s. 311-321
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Tidskriftsartikel (refereegranskat)abstract
- The cytochrome P4501 (CYP1) gene family comprises four subfamilies in fish: CYP1A, CYP1B, CYP1C, and CYP1D. Only two CYP1 genes, CYP1A1 and CYP1A3, are so far known in rainbow trout (Oncorhynchus mykiss). The present study aimed to identify other CYP1 subfamily genes in rainbow trout, to establish methods for quantitative mRNA expression analysis of these genes, and to determine their basal and induced mRNA expression in gills and liver. Another goal was to examine their mRNA expression in environmentally exposed fish. We cloned four new transcripts, denoted rbCYP1B1, rbCYP1C1, rbCYP1C2, and rbCYP1C3. Levels of these and the previously known rbCYP1A transcripts were determined by real-time PCR in unexposed fish, fish exposed to the potent aryl hydrocarbon receptor (AhR) agonist 3,3',4,4',5-pentachlorobiphenyl (PCB126), and fish caged in various waters in the Uppsala region (Sweden). The mRNA expression patterns observed in unexposed rainbow trout (basal levels) were markedly similar to those reported for orthologous genes in other species. All six transcripts were induced by PCB126 in gills and liver, suggesting all genes to be AhR regulated. The caged fish showed clear rbCYP1 induction in gills at all monitoring sites (up to 70-fold the basal level), whereas the liver responses were weak; induction (up to 5-fold) was recorded only at the Uppsala municipal sewage treatment plant outlet. Gill filament EROD activity was induced at all caging sites. Most interestingly, the rbCYP1 gene response patterns in gills differed among caging sites and among subfamilies. The EROD induction seemed to only reflect induction of rbCYP1A transcription. Response patterns of multiple CYP1 genes in gills and liver could provide an improved monitoring strategy. Such patterns could be used to characterize complex mixtures of AhR agonists and antagonists in aquatic environments.
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| 11. |
- Li, Jian, et al.
(författare)
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Array Comparative Genomic Hybridization of Keratoacanthomas and Squamous Cell Carcinomas: Different Patterns of Genetic Aberrations Suggest Two Distinct Entities
- 2012
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Ingår i: Journal of Investigative Dermatology. - : Elsevier BV. - 1523-1747 .- 0022-202X. ; 132:8, s. 2060-2066
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Tidskriftsartikel (refereegranskat)abstract
- Keratoacanthoma (KA) is a benign keratinocytic neoplasm that spontaneously regresses after 3-6 months and shares features with squamous cell carcinomas (SCCs). Furthermore, there are reports of KAs that have metastasized, invoking the question of whether KA is a variant of SCC (Hodak et al., 1993). To date, no reported criteria are sensitive enough to discriminate reliably between KA and SCC, and consequently there is a clinical need for discriminating markers. Our previous study analyzed 132 KAs and 29 SCCs and revealed significantly different regions of genomic aberrations using chromosomal comparative genomic hybridization (CGH). In the present study, we applied array CGH to investigate 98 KAs and 22 SCCs from the above samples. The result shows that all KAs and SCCs have some degree of genetic aberrations. The distribution of numbers of aberrant clones per sample differed significantly between KAs and SCCs (P<0.02), which also demonstrated recurrent aberrations that differed significantly (P<0.001), as illustrated by unsupervised cluster analysis. Classifiers for clinicopathological parameters of KAs were established based on t-test statistics and permutation tests. Tumor size, fibrosis, and inflammation, which are related to the developmental stages of KAs, showed significant (t-test, permutation test) associations with aberrations of selected genomic regions. This suggests chromosomal instability during the whole life cycle of KAs.
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| 12. |
- Sun, Bing, et al.
(författare)
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Wavelength-Spacing-Tunable Double-Pumped Multiwavelength Optical Parametric Oscillator Based on a Mach-Zehnder Interferometer
- 2012
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Ingår i: Journal of Lightwave Technology. - 0733-8724 .- 1558-2213. ; 30:12, s. 1937-1942
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Tidskriftsartikel (refereegranskat)abstract
- A novel double-pumped ring cavity multiwavelength fiber optical parametric oscillator (MW-FOPO) with tunable wavelength spacing is proposed. In the MW-FOPO, we utilize a highly nonlinear dispersion-shifted fiber as the gain medium and a Mach-Zehnder interferometer as the comb-like filter. Twenty-four-wavelength lasing of the double-pumped MW-FOPO with a ripple less than +/- 4.3 dB and a wavelength spacing of about 0.8 nm in a wavelength range from 1541 to 1558 nm is experimentally demonstrated. The wavelength spacing can be continuously tuned and multiwavelength lasings with wavelength spacings of 0.08, 0.2, 0.4, and 0.8 nm are demonstrated, respectively. We discussed the power stability of the multiwavelength lasing of the double-pumped MW-FOPO. A comparison of the output spectra among the double-pumped MW-FOPO, the single-pumped MW-FOPO, and the multiwavelength erbium-doped fiber laser is also presented.
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| 13. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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