| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 10. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 11. |
- Aad, G., et al.
(author)
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- 2014
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In: Physical Review C (Nuclear Physics). - 0556-2813 .- 1089-490X. ; 90:4
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Journal article (peer-reviewed)
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| 12. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 13. |
- Aad, G., et al.
(author)
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- 2014
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In: The European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6052. ; 74:10
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Journal article (peer-reviewed)
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| 14. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 15. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 16. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 17. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 18. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 19. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 20. |
- Aad, G., et al.
(author)
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- 2014
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In: The European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6052. ; 74:12
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Journal article (peer-reviewed)
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| 21. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 22. |
- Aad, G., et al.
(author)
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- 2014
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In: The European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6052. ; 74:11
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Journal article (peer-reviewed)
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| 23. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 24. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :9
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Journal article (peer-reviewed)
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| 25. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :11
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Journal article (peer-reviewed)
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| 26. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :10
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Journal article (peer-reviewed)
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| 27. |
- Aad, G., et al.
(author)
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- 2014
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In: Physical Review D. Particles and fields. - 0556-2821 .- 1089-4918. ; 90:11, s. 112006-
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Journal article (peer-reviewed)
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| 28. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :9, s. 1-61
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Journal article (peer-reviewed)
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| 29. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :8
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Journal article (peer-reviewed)
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| 30. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 31. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :9
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Journal article (peer-reviewed)
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| 32. |
- Aad, G., et al.
(author)
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- 2014
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In: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368 .- 1550-7998. ; 90:5
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Journal article (peer-reviewed)
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| 33. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :9
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Journal article (peer-reviewed)
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| 34. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :10
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Journal article (peer-reviewed)
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| 35. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :11
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Journal article (peer-reviewed)
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| 36. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :9
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Journal article (peer-reviewed)
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| 37. |
- Aad, G., et al.
(author)
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- 2014
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In: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368 .- 1550-7998. ; 90:5
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Journal article (peer-reviewed)
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| 38. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :9, s. 1-49
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Journal article (peer-reviewed)
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| 39. |
- Aad, G., et al.
(author)
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- 2014
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In: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368 .- 1550-7998. ; 90:11
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Journal article (peer-reviewed)
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| 40. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 41. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :10
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Journal article (peer-reviewed)
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| 42. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 43. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - : Springer Nature. - 1029-8479 .- 1126-6708. ; :11
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Journal article (peer-reviewed)
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| 44. |
- Aad, G, et al.
(author)
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- 2014
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In: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 113:17
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Journal article (peer-reviewed)
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| 45. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :11
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Journal article (peer-reviewed)
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| 46. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :9
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Journal article (peer-reviewed)
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| 47. |
- Aad, G., et al.
(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 48. |
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| 49. |
- Zhu, Haining, et al.
(author)
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EMMPRIN regulates cytoskeleton reorganization and cell adhesion in prostate cancer
- 2011
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In: The Prostate. - : Wiley. - 0270-4137 .- 1097-0045. ; 72:1, s. 72-81
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Journal article (peer-reviewed)abstract
- BACKGROUND: Proteins on cell surface play important roles during cancer progression and metastasis via their ability to mediate cell-to-cell interactions and navigate the communication between cells and the microenvironment. METHODS: In this study a targeted proteomic analysis was conducted to identify the differential expression of cell surface proteins in human benign (BPH-1) versus malignant (LNCaP and PC-3) prostate epithelial cells. We identified EMMPRIN (extracellular matrix metalloproteinase inducer) as a key candidate and shRNA functional approaches were subsequently applied to determine the role of EMMPRIN in prostate cancer cell adhesion, migration, invasion as well as cytoskeleton organization. RESULTS: EMMPRIN was found to be highly expressed on the surface of prostate cancer cells compared to BPH-1 cells, consistent with a correlation between elevated EMMPRIN and metastasis found in other tumors. No significant changes in cell proliferation, cell cycle progression, or apoptosis were detected in EMMPRIN knockdown cells compared to the scramble controls. Furthermore, EMMPRIN silencing markedly decreased the ability of PC-3 cells to form filopodia, a critical feature of invasive behavior, while it increased expression of cell-cell adhesion and gap junction proteins. CONCLUSIONS: Our results suggest that EMMPRIN regulates cell adhesion, invasion, and cytoskeleton reorganization in prostate cancer cells. This study identifies a new function for EMMPRIN as a contributor to prostate cancer cell-cell communication and cytoskeleton changes towards metastatic spread, and suggests its potential value as a marker of prostate cancer progression to metastasis.
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| 50. |
- Chen, Yancang, et al.
(author)
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A Trace-driven Hardware-level Simulator for Design and Verification of Network-on-Chips
- 2010
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In: 2011 INTERNATIONAL CONFERENCE ON COMPUTERS, COMMUNICATIONS, CONTROL AND AUTOMATION (CCCA 2011), VOL II. - : IEEE. ; , s. 32-35
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Conference paper (peer-reviewed)abstract
- Traditional communications of general-purpose multi-core processor and application-specific System-on-Chip face challenges in terms of scalability and complexity. Network-on-Chip (NoC) has been the most promising solution for the communications of multi-core and many-core chips. In this paper, we present a trace-driven hardware-level simulator (noted HS) based on SystemVerilog for the design and verification of NoCs. Different from the state-of-the-art NoC simulators, the HS owns three important characteristics in addition to the capability of creating simulation and synthesizable NoC descriptions: 1) hardware-level simulation can be done, which means more implementation details of hardware than flit-level simulation; 2) router debugging and verification can be done at RTL by inserting assertions and coverage; 3) trace-based application simulations can be done besides synthetic workloads. A 4 X 4 2D mesh NoC with output virtual-channel routers verifies the capability of our HS.
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