| 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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| 2. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 3. |
- Lee, Dung-Fang, et al.
(author)
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Regulation of embryonic and induced pluripotency by aurora kinase-p53 signaling.
- 2012
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In: Cell Stem Cell. - : Elsevier BV. - 1934-5909 .- 1875-9777. ; 11:2
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Journal article (peer-reviewed)abstract
- Many signals must be integrated to maintain self-renewal and pluripotency in embryonic stem cells (ESCs) and to enable induced pluripotent stem cell (iPSC) reprogramming. However, the exact molecular regulatory mechanisms remain elusive. To unravel the essential internal and external signals required for sustaining the ESC state, we conducted a short hairpin (sh) RNA screen of 104 ESC-associated phosphoregulators. Depletion of one such molecule, aurora kinase A (Aurka), resulted in compromised self-renewal and consequent differentiation. By integrating global gene expression and computational analyses, we discovered that loss of Aurka leads to upregulated p53 activity that triggers ESC differentiation. Specifically, Aurka regulates pluripotency through phosphorylation-mediated inhibition of p53-directed ectodermal and mesodermal gene expression. Phosphorylation of p53 not only impairs p53-induced ESC differentiation but also p53-mediated suppression of iPSC reprogramming. Our studies demonstrate an essential role for Aurka-p53 signaling in the regulation of self-renewal, differentiation, and somatic cell reprogramming.
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| 4. |
- Lou, H. B., et al.
(author)
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Pressure-induced amorphous-to-amorphous configuration change in Ca-Al metallic glasses
- 2012
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 2, s. 376-
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Journal article (peer-reviewed)abstract
- Pressure-induced amorphous-to-amorphous configuration changes in Ca-Al metallic glasses (MGs) were studied by performing in-situ room-temperature high-pressure x-ray diffraction up to about 40 GPa. Changes in compressibility at about 18 GPa, 15.5 GPa and 7.5 GPa during compression are detected in Ca80Al20, Ca72.7Al27.3, and Ca66.4Al33.6 MGs, respectively, whereas no clear change has been detected in the Ca50Al50 MG. The transfer of s electrons into d orbitals under pressure, reported for the pressure-induced phase transformations in pure polycrystalline Ca, is suggested to explain the observation of an amorphous-to-amorphous configuration change in this Ca-Al MG system. Results presented here show that the pressure induced amorphous-to-amorphous configuration is not limited to f electron-containing MGs.
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| 5. |
- Piao, S. L., et al.
(author)
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The carbon budget of terrestrial ecosystems in East Asia over the last two decades
- 2012
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In: Biogeosciences. - : Copernicus GmbH. - 1726-4189. ; 9:9, s. 3571-3586
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Journal article (peer-reviewed)abstract
- This REgional Carbon Cycle Assessment and Processes regional study provides a synthesis of the carbon balance of terrestrial ecosystems in East Asia, a region comprised of China, Japan, North and South Korea, and Mongolia. We estimate the current terrestrial carbon balance of East Asia and its driving mechanisms during 1990-2009 using three different approaches: inventories combined with satellite greenness measurements, terrestrial ecosystem carbon cycle models and atmospheric inversion models. The magnitudes of East Asia's terrestrial carbon sink from these three approaches are comparable: -0.293 +/- 0.033 PgC yr(-1) from inventory-remote sensing model-data fusion approach, -0.413 +/- 0.141 PgC yr(-1)(not considering biofuel emissions) or -0.224 +/- 0.141 PgC yr(-1) (considering biofuel emissions) for carbon cycle models, and -0.270 +/- 0.507 PgC yr(-1) for atmospheric inverse models. Here and in the following, the numbers behind +/- signs are standard deviations. The ensemble of ecosystem modeling based analyses further suggests that at the regional scale, climate change and rising atmospheric CO2 together resulted in a carbon sink of -0.289 +/- 0.135 PgC yr(-1), while land-use change and nitrogen deposition had a contribution of -0.013 +/- 0.029 PgC yr(-1) and -0.107 +/- 0.025 PgC yr(-1), respectively. Although the magnitude of climate change effects on the carbon balance varies among different models, all models agree that in response to climate change alone, southern China experienced an increase in carbon storage from 1990 to 2009, while northern East Asia including Mongolia and north China showed a decrease in carbon storage. Overall, our results suggest that about 13-27% of East Asia's CO2 emissions from fossil fuel burning have been offset by carbon accumulation in its terrestrial territory over the period from 1990 to 2009. The underlying mechanisms of carbon sink over East Asia still remain largely uncertain, given the diversity and intensity of land management processes, and the regional conjunction of many drivers such as nutrient deposition, climate, atmospheric pollution and CO2 changes, which cannot be considered as independent for their effects on carbon storage.
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| 6. |
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| 7. |
- Zhao, Zeng-Ren, et al.
(author)
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Increased serum level of Nup88 protein is associated with the development of colorectal cancer
- 2012
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In: Medical Oncology. - : Humana Press (Springer Imprint). - 1357-0560 .- 1559-131X. ; 29:3, s. 1789-1795
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Journal article (peer-reviewed)abstract
- Nucleoporin88 (Nup88) has been shown to be overexpressed in a wide variety of malignancies including colorectal cancer (CRC). However, no study about serum Nup88 in human CRC was reported. Therefore, in this study, we investigated the level of serum Nup88 protein and its relationships with clinicopathological variables in CRC. The serum concentration of Nup88 protein was determined by a quantitative sandwich enzyme-linked immunosorbent assay (ELISA) in 118 pre-operative serum samples, 66 post-operative and 96 healthy controls. Among the patients, the levels of CEA (n = 91) and CA19-9 (n = 87) in the pre-operative serum were measured, and DNA sequencing was performed in 12 CRCs and 2 samples from non-cancerous colon tissue. In the same patients, the level of pre-operative serum Nup88 was significantly higher than that of post-operative Nup88 (P = 0.021). Furthermore, the level of pre-operative Nup88 was positively related to the depth of tumor invasion (P = 0.002) and advanced stage (P = 0.001). The level of pre-operative Nup88 in the left colon tended to be higher than that in the right colon and the rectum (P = 0.063). DNA sequencing results showed that there were two single nucleotide polymorphisms, distributed in exon 6 (NM_002532.3:c.1044Gandgt;A (ACG-ACA, Thr -andgt; Thr) and exon 10 (NM_002532.3: c.1389Aandgt;T, CCA-CCT, Pro -andgt; Pro). Serum Nup88 might be a candidate for a new biomarker implicated in the development and aggressiveness of CRCs.
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| 8. |
- Zhu, Dechun, et al.
(author)
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The influence of oxygen in TiAlOxNy on the optical properties of colored solar-absorbing coatings
- 2012
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In: Solar Energy Materials and Solar Cells. - Amsterdam : Elsevier. - 0927-0248 .- 1879-3398. ; 98, s. 179-184
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Journal article (peer-reviewed)abstract
- Low cost and ease of fabrication are important factors for solar-thermal applications in energy-efficient buildings. This contribution reports the influence of oxygen on structure, optical properties and chromaticity of TiAlOxNy thin films prepared by DC magnetron sputtering. It is an extension of a previous study on colored solar-thermal absorbers based on titanium-aluminum nitride. The purpose is to investigate the possibility of using TiAlOxNy as middle layer to achieve a gradient effect. The results reveal that the structure and optical properties of the TiAlOxNy coatings are sensitive to the oxygen content under certain sputtering conditions. The ratio of oxygen/nitrogen of 0.7:10 is the most appropriate to form the crystalline structure of TiAlON. The optical constants of TiAlN and TiAlON were deduced by fitting the experimental data. It shows that both the refractive index (n) and the extinction coefficient (k) are decreased when oxygen is introduced to form titanium-aluminium nitro-oxide. The gradient effect can be achieved and controlled by adjusting the ratio of oxygen/nitrogen flow during the process to enhance solar absorptance while keeping the desired color appearance.
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