| 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. |
- 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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| 3. |
- Chen, Mei-Qin, et al.
(författare)
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Arabidopsis NMD3 is required for nuclear export of 60S ribosomal subunits and affects secondary cell wall thickening
- 2012
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:4, s. 35904-35904
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Tidskriftsartikel (refereegranskat)abstract
- NMD3 is required for nuclear export of the 60S ribosomal subunit in yeast and vertebrate cells, but no corresponding function of NMD3 has been reported in plants. Here we report that Arabidopsis thaliana NMD3 (AtNMD3) showed a similar function in the nuclear export of the 60S ribosomal subunit. Interference with AtNMD3 function by overexpressing a truncated dominant negative form of the protein lacking the nuclear export signal sequence caused retainment of the 60S ribosomal subunits in the nuclei. More interestingly, the transgenic Arabidopsis with dominant negative interference of AtNMD3 function showed a striking failure of secondary cell wall thickening, consistent with the altered expression of related genes and composition of cell wall components. Observation of a significant decrease of rough endoplasmic reticulum (RER) in the differentiating interfascicular fiber cells of the transgenic plant stems suggested a link between the defective nuclear export of 60S ribosomal subunits and the abnormal formation of the secondary cell wall. These findings not only clarified the evolutionary conservation of NMD3 functions in the nuclear export of 60S ribosomal subunits in yeast, animals and plants, but also revealed a new facet of the regulatory mechanism underlying secondary cell wall thickening in Arabidopsis. This new facet is that the nuclear export of 60S ribosomal subunits and the formation of RER may play regulatory roles in coordinating protein synthesis in cytoplasm and transcription in nuclei.
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| 4. |
- 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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| 5. |
- Cao, H. W., et al.
(författare)
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Magnetic properties in (Mn,Fe)-codoped ZnO nanowire
- 2013
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Ingår i: Thin Solid Films. - : Elsevier BV. - 0040-6090. ; 548, s. 480-484
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Tidskriftsartikel (refereegranskat)abstract
- Using the first-principles density functional theory, we have studied the electronic structures and magnetic properties of Mn/Fe codoped ZnO nanowires systematically. The calculated results of formation energy indicate that the configuration of the lowest energy where Mn and Fe atoms form nearest neighbors on the outer cylindrical surface layer along the [0001] direction, will be determined. The magnetic coupling of 8 types of Mn/Fe codoped ZnO nanowires was investigated and ferromagnetic state was found in certain configurations. The mechanism is from the fierce hybridization between 3d of Mn and Fe with O 2p near the Fermi level. The relative energy difference for configuration VIII is 0.221 eV, which indicates that room temperature ferromagnetism could be obtained in such a system and Mn/Fe codoped ZnO nanowires are a promising nanoscale spintronic material. (C) 2013 Elsevier B. V. All rights reserved.
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| 6. |
- Leng, Xue-Li, et al.
(författare)
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Spiral Coil Inserts for Heat Transfer Enhancement in a Parallel-plate Channel
- 2014
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Ingår i: Numerical Heat Transfer Part A: Applications. - : Informa UK Limited. - 1040-7782 .- 1521-0634. ; 66:7, s. 756-772
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Tidskriftsartikel (refereegranskat)abstract
- The flow fields and heat transfer characteristics in a parallel-plate channel with a transversely placed spiral coil insert were investigated by three-dimensional numerical simulation. The structure of multi-longitudinal-vortices (MLVs) induced by the spiral coil and the effects of MLVs on velocity and temperature fields were studied. The three-dimensional spiral coil induces a series of longitudinal vortices in the channel including leading longitudinal vortex, mainstream longitudinal vortices, near-wall longitudinal vortices, and rear central longitudinal vortex. Transport by the longitudinal vortices can increase the mass exchange between the boundary layer and the mainstream, which speeds up the heat migration from the channel walls and enhances the heat diffusion in the mainstream.
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| 7. |
- Wang, Yaling, et al.
(författare)
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Enhanced performance and stability in polymer photovoltaic cells using lithium benzoate as cathode interfacial layer
- 2011
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Ingår i: SOLAR ENERGY MATERIALS AND SOLAR CELLS. - : Elsevier Science B.V., Amsterdam.. - 0927-0248. ; 95:4, s. 1243-1247
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Tidskriftsartikel (refereegranskat)abstract
- We report the enhanced performance and stability of polymer solar cells based on regioregular poly(3-hexylthiophene)(P3HT) and methanofullerene [6,6]-phenyl C-61-butyric acid methyl ester (PCBM) blend using lithium benzoate (C6H5COOLi) as cathode buffer layer between the active layer and the Al cathode. The effects of the C6H5COOLi thickness on the performance of polymer solar cell are also investigated. Under 100 mW/cm(2) white light illumination, the device with 1 nm thick C6H5COOLi as cathode buffer layer exhibits power conversion efficiency (PCE) as high as 3.41 +/- 0.07% and the device stability is greatly extended. Compared to the solar cell with LiF/AI cathode, the PCE is increased ca. 9.4%. Introduction of C6H5COOLi buffer layer effectively increases the shunt resistance and improves the photo-generated charge collection. The improved performance may attribute to the dissociation of semi-conducting C6H5COOLi upon deposition to liberate Li with a low work function, which reduces the interface resistance of the active layer and the cathode and enhances the interior electric field that may result in efficient charge transportion. In addition, the C6H5COOLi layer may serve as an effective oxygen and moisture diffusion barrier for the organic solar cells. Therefore. C6H5COOLi is a promising candidate as an interlayer to improve the efficiency of electron collection and to reduce the ambience influence on the stability of polymer solar cells.
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| 8. |
- 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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| 9. |
- Zhang, Mengmeng, et al.
(författare)
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Hybrid feedback design for subsonic and transonic airfoils and wings
- 2014
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Ingår i: 52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014. - National Harbor : American Institute of Aeronautics and Astronautics.
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Konferensbidrag (refereegranskat)abstract
- A hybrid inverse/optimization method for subsonic/transonic airfoil and wing shapedesign is presented with application to a range of airfoil and wing cases, in preparation forthe test cases defined for the Special Session of SciTech 2014. The method is hybrid in thesense that it combines the traditional inverse design technique with an optimization pro-cedure that determines the optimum target pressure distribution. This paper emphasizesthe first part, the development of SCID, the Surface Curvature Inverse Design method,the theory upon which it is based, including many of the details involved with shocks,smoothing and cross flow. The application of SCID to wing design poses many challenges,and how they are met is discussed in the context of a number of inverse design test casesfor airfoils and wings. The procedure works well for airfoils, whereas twist optimizationfor transonic wings remains a challenge. The real benchmarks for our hybrid approach arethe three Optimization Discussion Group design problems. Solutions are presented for thedrag minimization of the NACA airfoil along with the wing twist optimization problem,and conclusions are drawn from the results obtained. Work has started on the drag mini-mization of the CRM wing in transonic flight, and final results will be presented in a futurepaper.
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| 10. |
- Zhang, Mengmeng, et al.
(författare)
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Variable fidelity methods and surrogate modeling of critical loads on X-31 aircraft
- 2013
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Ingår i: 51st AIAA Aerospace Sciences Meeting including the New Horizons Forum and Aerospace Exposition 2013. - Reston, Virigina : American Institute of Aeronautics and Astronautics. - 9781624101816
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Konferensbidrag (refereegranskat)abstract
- This paper presents a method for effcient creation of the aerodynamic database for the X-31 experimental aircraft, from low fidelity (Euler) and high fidelity (RANS) CFD. The challenge is to obtain good data for extreme flight conditions. A co-Kriging interpolation model for aerodynamic moments, forces and span loads is used, with an additional decision support system (DSS) using Proper Orthogonal Decomposition for data reduction.
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