| 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. |
- Liao, Shih-Fen, et al.
(författare)
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Immunization of fucose-containing polysaccharides from Reishi mushroom induces antibodies to tumor-associated Globo H-series epitopes.
- 2013
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 110:34, s. 13809-13814
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Tidskriftsartikel (refereegranskat)abstract
- Carbohydrate-based vaccines have shown therapeutic efficacy for infectious disease and cancer. The mushroom Ganoderma lucidum (Reishi) containing complex polysaccharides has been used as antitumor supplement, but the mechanism of immune response has rarely been studied. Here, we show that the mice immunized with a l-fucose (Fuc)-enriched Reishi polysaccharide fraction (designated as FMS) induce antibodies against murine Lewis lung carcinoma cells, with increased antibody-mediated cytotoxicity and reduced production of tumor-associated inflammatory mediators (in particular, monocyte chemoattractant protein-1). The mice showed a significant increase in the peritoneal B1 B-cell population, suggesting FMS-mediated anti-glycan IgM production. Furthermore, the glycan microarray analysis of FMS-induced antisera displayed a high specificity toward tumor-associated glycans, with the antigenic structure located in the nonreducing termini (i.e., Fucα1-2Galβ1-3GalNAc-R, where Gal, GalNAc, and R represent, respectively, D-galactose, D-N-acetyl galactosamine, and reducing end), typically found in Globo H and related tumor antigens. The composition of FMS contains mainly the backbone of 1,4-mannan and 1,6-α-galactan and through the Fucα1-2Gal, Fucα1-3/4Man, Fucα1-4Xyl, and Fucα1-2Fuc linkages (where Man and Xyl represent d-mannose and d-xylose, respectively), underlying the molecular basis of the FMS-induced IgM antibodies against tumor-specific glycans.
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| 3. |
- An, Junghwa, et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
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| 4. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Tidskriftsartikel (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 5. |
- Lin, Ke, et al.
(författare)
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Identification of Free OH and its Implication on Structural Changes of Liquid Water
- 2013
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Ingår i: Chinese Journal of Chemical Physics. - : AIP Publishing. - 1674-0068 .- 2327-2244. ; 26:2, s. 121-126
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Tidskriftsartikel (refereegranskat)abstract
- The molecular structure of liquid water has been an outstanding issue for many years. The identification of free -OH holds the key in differentiating structure models for liquid water. By analyzing the relative changes of the intensity and depolarization ratio in temperature dependent Raman spectra, the occurrence of free -OH in liquid water is unambiguously determined. Furthermore, upon the increase of temperature from 5 degrees C to 85 degrees C, the structure of liquid water undergoes significant change, but the relative proportion of free -OH is considerably small and remains almost unchanged. This implies that the breaking of hydrogen bond from the tetrahedral structure prefers to occur at the site of the hydrogen acceptor. The energetic favoring of the structural change for liquid water is thus clearly revealed from experiments.
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| 6. |
- Lin, Ke, et al.
(författare)
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Quantum Effects on Global Structure of Liquid Water
- 2013
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Ingår i: Chinese Journal of Chemical Physics. - : AIP Publishing. - 1674-0068 .- 2327-2244. ; 26:2, s. 127-132
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Tidskriftsartikel (refereegranskat)abstract
- The structure difference between light and heavy liquid water has been systematically investigated by high precision Raman. spectroscopy over the temperature range of 5-85 degrees C. Distinct difference between the Raman spectral profiles of two different liquid waters is clearly observed. By analyzing the temperature-dependent Raman spectral contour using global fitting procedure, it is found that the micro-structure of heavy water is more ordered than that of light water at the same temperature, and the structure difference between the light and heavy water decreases with the increase of the temperature. The temperature offset, an indicator for the structure difference, is determined to vary from 28 degrees C to 18 degrees C for the low-to-high temperature. It indicates that quantum effect is significantly not only at low temperature, but also at room temperature. The interaction energy among water molecules has also been estimated from van't Hoff's relationship. The detailed structural information should help to develop reliable force fields for molecular modeling of liquid water.
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| 7. |
- Li, Hongbao, et al.
(författare)
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Gas-phase IR spectroscopy of deprotonated amino acids : Global or Local minima?
- 2014
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 598, s. 86-90
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Tidskriftsartikel (refereegranskat)abstract
- Density functional theory calculations for the structure and IR spectroscopy of deprotonated tyrosine and cysteine molecules in gas phase have been carried out to resolve the on-going debate about the global minimum of deprotonated amino acids. It is found that the global minimum of the deprotonated specie is not always directly produced from the most stable neutral conformer. Depending on the setup, the experimental IR spectroscopy of deprotonated amino acids could only give the information of the local minima of the deprotonated species.
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| 8. |
- Li, Hongbao, et al.
(författare)
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The Role of Dimerization on the Structure Transformation of Arginine in Gas Phase
- 2014
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Ingår i: Chemical Physics Letters. - Elsevier : Elsevier BV. - 0009-2614 .- 1873-4448. ; 608, s. 398-403
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Tidskriftsartikel (refereegranskat)abstract
- The equilibrium distribution of arginine molecules in canonical and zwitterionicforms predicted by the theory failed to correctly reproduce the double-peak feature observedin the IR experiment. We have shown from first principles calculations that the energeticallyfavorable dimerization of zwitterions can effectively eliminate the pathway for the structureconversion between two distinct canonical forms and reduce the probability for thesecanonical forms to reach their thermal equilibrium. The role of dispersion effect is discussed.It suggests that the experimental IR spectrum is determined by the way how the conformersof arginine are initially generated.
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| 9. |
- Hsiung, Te-Chih, et al.
(författare)
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Enhanced surface mobility and quantum oscillations in topological insulator Bi1.5Sb0.5Te1.7Se1.3 nanoflakes
- 2013
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 103:16
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Tidskriftsartikel (refereegranskat)abstract
- n this study, a series of Bi1.5Sb0.5Te 1.7Se1.3 (BSTS) flakes 80-nm to 140-μm in thickness was fabricated to investigate their metallic surface states. We report the observation of surface-dominated transport in these topological insulator BSTS nanoflakes. The achievement of surface-dominated transport can be attributed to high surface mobility (∼3000 cm2/V s) and low bulk mobility (12 cm2/V s). Up to 90% of the total conductance, the surface channel was estimated based on the thickness dependence of electrical conductance and the result of the Shubnikov-de Hass oscillations in a 200-nm BSTS. The nature of nontrivial Dirac surface states was also confirmed by the weak anti-localization effect.
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| 10. |
- Aaltonen, T., et al.
(författare)
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Combination of CDF and D0 measurements of the W boson helicity in top quark decays
- 2012
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 85:7, s. 071106-
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Tidskriftsartikel (refereegranskat)abstract
- We report the combination of recent measurements of the helicity of the W boson from top quark decay by the CDF and D0 collaborations, based on data samples corresponding to integrated luminosities of 2.7-5.4 fb(-1) of p (p) over bar collisions collected during Run II of the Fermilab Tevatron collider. Combining measurements that simultaneously determine the fractions of W bosons with longitudinal (f(0)) and right-handed (f(+)) helicities, we find f(0) = 0.722 +/- 0.081[+/- 0.062(stat) +/- 0.052(syst)] and f(+) = -0.033 +/- 0.046[+/- 0.034(stat) +/- 0.031(syst)]. Combining measurements where one of the helicity fractions is fixed to the value expected in the standard model, we find f(0) = 0.682 +/- 0.057[+/- 0.035(stat) +/- 0.046(syst)] for fixed f(+) and f(+) = -0.015 +/- 0.035[+/- 0.018(stat) +/- 0.030(syst)] for fixed f(0). The results are consistent with standard model expectations.
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