| 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. |
- Anderson, Cynthia M., et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:3, s. 576-579
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mulleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.
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| 3. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 4. |
- Baran, J. D., et al.
(författare)
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Theoretical and experimental comparison of SnPc, PbPc, and CoPc adsorption on Ag(111)
- 2010
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121 .- 1550-235X. ; 81:7
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Tidskriftsartikel (refereegranskat)abstract
- A combination of normal-incidence x-ray standing-wave (NIXSW) spectroscopy, x-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and density-functional theory (DFT) has been used to investigate the interaction of a number of phthalocyanine molecules (specifically, SnPc, PbPc, and CoPc) with the Ag(111) surface. The metal-surface distances predicted by the DFT calculations for SnPc/Ag(111) (2.48 angstrom) and CoPc/Ag(111) (2.88 angstrom) are in good agreement with our NIXSW experimental results for these systems (2.31 +/- 0.09 and 2.90 +/- 0.05 angstrom, respectively). Good agreement is also found between calculated partial density-of-states plots and STM images of CoPc on Ag(111). Although the DFT and Pb 4f NIXSW results for the Pb-Ag(111) distance are similarly in apparently good agreement, the Pb 4f core-level data suggest that a chemical reaction between PbPc and Ag(111) occurs due to the annealing procedure used in our experiments and that the similarity of the DFT and Pb 4f NIXSW values for the Pb-Ag(111) distance is likely to be fortuitous. We interpret the Pb 4f XPS data as indicating that the Pb atom can detach from the PbPc molecule when it is adsorbed in the "Pb-down" position, leading to the formation of a Pb-Ag alloy and the concomitant reduction in Pb from a Pb2+ state (in bulklike films of PbPc) to Pb-0. In contrast to SnPc, neither PbPc nor CoPc forms a well-ordered monolayer on Ag(111) via the deposition and annealing procedures we have used. Our DFT calculations show that each of the phthalocyanine molecules donate charge to the silver surface, and that back donation from Ag to the metal atom (Co, Sn, or Pb) is only significant for CoPc.
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| 5. |
- Feng, Yi, et al.
(författare)
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The onset of human ectopic pregnancy demonstrates a differential expression of miRNAs and their cognate targets in the Fallopian tube
- 2014
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Ingår i: International Journal of Clinical and Experimental Pathology. - 1936-2625. ; 7:1, s. 64-79
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Tidskriftsartikel (refereegranskat)abstract
- Human ectopic pregnancy (EP) is a leading cause of pregnancy-related death, but the molecular basis underlying the onset of tubal EP is largely unknown. Female Dicer1 conditional knockout mice are infertile with dysfunctional Fallopian tube and have a different miRNA expression profile compared to wild-type mice, and we speculated that Dicer-mediated regulation of miRNA expression and specific miRNA-controlled targets might contribute to the onset of tubal EP. In the present study, we used microarray analysis and quantitative RT-PCR to examine the expression of miRNAs and core miRNA regulatory components in Fallopian tube tissues from women with EP. We found that the levels of DICER1, four miRNAs (let-7i, miR-149, miR-182, and miR-424), and estrogen receptor α distinguished the tubal implantation site from the non-implantation site. Computational algorithms and screening for interactions with the estrogen and progesterone receptor signaling pathways showed that the four miRNAs were predicted to target ten genes, including NEDD4, TAF15, and SPEN. Subsequent experiments showed differences in NEDD4 mRNA and protein levels between the implantation and non-implantation sites. Finally, we revealed that increases in smooth muscle cell NEDD4 and stromal cell TAF15, in parallel with a decrease in epithelial cell SPEN, were associated with tubal implantation. Our study suggests that changes in miRNA levels by the DICER-mediated miRNA-processing machinery result in aberrant expression of cell type-specific proteins that are potentially involved in the onset of tubal EP.
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| 6. |
- Ha, H., et al.
(författare)
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Effect of applied potential on Pit propagation in copper as function of water chemistry
- 2012
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Ingår i: Journal of the Electrochemical Society. - : The Electrochemical Society. - 0013-4651 .- 1945-7111. ; 159:2, s. C59-C73
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Tidskriftsartikel (refereegranskat)abstract
- The effect of potential on pit propagation as a function of water chemistry was investigated using artificial pit electrodes. In both 0.01 M HCO 3 - 0.01 M SO 4 2- and 0.01 M HCO 3 - 0.01 M Cl - solutions, pits grew faster at higher applied potentials. However the magnitude of the pitting rate depends on the solution chemistry. A higher pitting rate was observed during pit growth in 0.01 M HCO 3 - 0.01 M SO 4 2- solution compared to 0.01 M HCO 3 - 0.01 M Cl - solution. The chemistry of the water determined the morphology and the molecular identity of corrosion products deposited inside and outside of the pits. Thick and porous layers of malachite and brochantiteposnjakite covered pits in 0.01 M HCO 3 - 0.01 M SO 4 2- solution. In contrast, thin and compact layers of malachite, cuprite and atacamitenantokiteeriochantite covered pits in 0.01 M HCO 3 - 0.01 M Cl - solution. Modeling successfully predicted these corrosion products. Applied potential determined the amount, the structure and the distribution of corrosion products in both experiment and model. However, the effect of potential was more pronounced in 0.01 M HCO 3 - 0.01 M SO 4 2- solution in comparison to 0.01 M HCO 3 - 0.01 M Cl - solution. © 2011 The Electrochemical Society.
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| 7. |
- Liu, J., et al.
(författare)
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Solvent-free ionic liquid electrolytes without elemental iodine for dye-sensitized solar cells
- 2012
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 14:33, s. 11592-11595
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Tidskriftsartikel (refereegranskat)abstract
- A new type of electrolyte with a sulfide/polysulfide redox couple and I - was prepared as a solvent-free ionic liquid for application in dye-sensitized solar cells, reaching efficiencies of 5.2-6.4% under AM 1.5G, 100 mW cm -2 light illumination, and 6.6% efficiency was obtained under 0.1 sun irradiation.
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| 8. |
- Murphy, Laurel E., et al.
(författare)
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Folate and vitamin B-12 in idiopathic male infertility
- 2011
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Ingår i: Asian Journal of Andrology. - : Medknow. - 1008-682X .- 1745-7262. ; 13:6, s. 856-861
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Tidskriftsartikel (refereegranskat)abstract
- Although methylenetetrahydrofolate reductase, a folate enzyme gene, has been associated with idiopathic male infertility, few studies have examined other folate-related metabolites and genes. We investigated whether idiopathic male infertility is associated with variants in folate, vitamin B-12 (B12) and total homocysteine (tHcy)-related genes and measured these metabolites in blood. We conducted a case-control study that included 153 men with idiopathic infertility and 184 fertile male controls recruited at the Fertility Center and Antenatal Care Center, University Hospital, Malmo and Lund, Sweden. Serum folate, red cell folate (RCF), serum B12, plasma tHcy and semen quality were measured. Subjects were genotyped for 20 common variants in 12 genes related to folate/B12/homocysteine metabolism. Metabolite concentrations and genotype distributions were compared between cases and controls using linear and logistic regression with adjustment for covariates. The phosphatidylethanolamine N-methyltransferase (PEMT) M175V and TCblR rs173665 polymorphisms were significantly associated with infertility (P=0.01 and P=0.009, respectively), but not with semen quality. Among non-users of supplements, infertile men had lower serum folate concentrations than fertile men (12.89 vs. 14.73 nmol l(-1); P=0.02), but there were no significant differences in RCF, B12 or tHcy. Folate, B12 and tHcy concentrations were not correlated with any semen parameters. This study provides little support for low folate or B12 status in the pathogenesis of idiopathic male infertility. Although additional data are needed to confirm these initial findings, our results suggest that PEMT and TCblR, genes involved in choline and B12 metabolism, merit further investigation in idiopathic male infertility. Asian Journal of Andrology (2011) 13, 856-861; doi: 10.1038/aja.2011.96; published online 22 August 2011
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| 9. |
- Toftegaard, R., et al.
(författare)
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Metal nanoparticle-enhanced radiative transitions: Giving singlet oxygen emission a boost
- 2011
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Ingår i: Pure and Applied Chemistry. - : Walter de Gruyter GmbH. - 1365-3075 .- 0033-4545. ; 83:4, s. 885-898
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Tidskriftsartikel (refereegranskat)abstract
- The fabrication and use of metal nanoparticles to influence electronic transitions in a given molecule is of growing interest; there is much to be gained by developing and exploiting methods to enhance weak optical signals. Singlet molecular oxygen, O-2(a(1)Delta(g)), which is an important intermediate in many oxidation reactions, particularly in biological systems, is ideally monitored by the 1275-nm O-2(a(1)Delta(g)) -> O-2(X-3 Sigma(-)(g)) phosphorescent transition. Unfortunately, the latter is highly forbidden and, as such, often presents a severe limitation in the application of this optical probe. In this paper, we describe how this weak phosphorescent transition can be enhanced by using localized surface plasmons (LSPs) from specially engineered gold nanostructures. In an attempt to elucidate the mechanism of this process, data were recorded from samples in which we decoupled the component of the plasmon resonance that absorbs incident light from the component that scatters incident light. We find that the latter appears to be the feature of significance in the process through which singlet oxygen phosphorescence is enhanced. In this work, we also illustrate how the singlet oxygen system provides an ideal model for a general study of metal-enhanced radiative rate constants.
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| 10. |
- Wei, Hong, et al.
(författare)
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Quantum Dot-Based Local Field Imaging Reveals Plasmon-Based Interferometric Logic in Silver Nanowire Networks
- 2011
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 11:2, s. 471-475
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Tidskriftsartikel (refereegranskat)abstract
- We show that the local electric field distribution of propagating plasmons along silver nanowires can be imaged by coating the nanowires with a layer of quantum dots, held off the surface of the nanowire by a nanoscale dielectric spacer layer. In simple networks of silver nanowires with two optical inputs, control of the optical polarization and phase of the input fields directs the guided waves to a specific nanowire output. The QD-luminescent images of these structures reveal that a complete family of phase-dependent, interferometric logic functions can be performed on these simple networks. These results show the potential for plasmonic waveguides to support compact interferometric logic operations.
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