| 1. |
- Klionsky, Daniel J., et al.
(author)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
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.
|
|
| 2. |
- Weinstein, John N., et al.
(author)
-
The cancer genome atlas pan-cancer analysis project
- 2013
-
In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
-
Research review (peer-reviewed)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.
|
|
| 3. |
- Chen, Xi, et al.
(author)
-
Ordered Au nanocrystals on a substrate formed by light-induced rapid annealing
- 2014
-
In: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 6:3, s. 1756-1762
-
Journal article (peer-reviewed)abstract
- Light-induced rapid annealing (LIRA) is a widely used method to modify the morphology and crystallinity of noble metal nanoparticles, and the nanoparticles generally evolve into nanospheres. It is rather challenging to form faceted Au nanocrystals on a substrate using LIRA. Here the formation of spatially ordered Au nanocrystals using a continuous wave infrared laser is reported, assisted by a metamaterial perfect absorber. Faceted Au nanocrystals in truncated-octahedral or multi-twinned geometries can be obtained. The evolution of morphology and crystallinity of the Au nanoparticles during laser annealing is also revealed, where the crystal grain growth and the surface melting are shown to play key roles in nanocrystal formation. The evolution of morphology also gives the freedom of tuning the absorption spectrum of the metamaterial absorber. These findings provide a novel way for tailoring the morphology and crystallinity of metallic nanoparticles and may pave the way to fabricate refined nano-devices in many potential applications for optics, electronics, catalysis, surface-chemistry and biology.
|
|
| 4. |
- Chu, Liliang, et al.
(author)
-
Biocompatible near-infrared fluorescent nanoparticles for macro and microscopic in vivo functional bioimaging
- 2014
-
In: Biomedical Optics Express. - 2156-7085. ; 5:11, s. 4076-4088
-
Journal article (peer-reviewed)abstract
- Near-infrared (NIR) imaging technology has been widely used for biomedical research and applications, since it can achieve deep penetration in biological tissues due to less absorption and scattering of NIR light. In our research, polymer nanoparticles with NIR fluorophores doped were synthesized. The morphology, absorption/emission features and chemical stability of the fluorescent nanoparticles were characterized, separately. NIR fluorescent nanoparticles were then utilized as bright optical probes for macro in vivo imaging of mice, including sentinel lymph node (SLN) mapping, as well as distribution and excretion monitoring of nanoparticles in animal body. Furthermore, we applied the NIR fluorescent nanoparticles in in vivo microscopic bioimaging via a confocal microscope. Under the 635 nm-CW excitation, the blood vessel architecture in the ear and the brain of mice, which were administered with nanoparticles, was visualized very clearly. The imaging depth of our one-photon microscopy, which was assisted with NIR fluorescent nanoprobes, can reach as deep as 500 mu m. Our experiments show that NIR fluorescent nanoparticles have great potentials in various deep-tissue imaging applications.
|
|
| 5. |
- Deng, Min, et al.
(author)
-
Genome-wide association analyses in Han Chinese identify two new susceptibility loci for amyotrophic lateral sclerosis
- 2013
-
In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 45:6, s. 697-
-
Journal article (peer-reviewed)abstract
- To identify susceptibility genes for amyotrophic lateral sclerosis (ALS), we conducted a genome-wide association study (GWAS) in 506 individuals with sporadic ALS and 1,859 controls of Han Chinese ancestry. Ninety top SNPs suggested by the current GWAS and 6 SNPs identified by previous GWAS were analyzed in an independent cohort of 706 individuals with ALS and 1,777 controls of Han Chinese ancestry. We discovered two new susceptibility loci for ALS at 1q32 (CAMK1G, rs6703183, P-combined = 2.92 x 10(-8), odds ratio (OR) = 1.31) and 22p11 (CABIN1 and SUSD2, rs8141797, P-combined = 2.35 x 10(-9), OR = 1.52). These two loci explain 12.48% of the overall variance in disease risk in the Han Chinese population. We found no association evidence for the previously reported loci in the Han Chinese population, suggesting genetic heterogeneity of disease susceptibility for ALS between ancestry groups. Our study identifies two new susceptibility loci and suggests new pathogenic mechanisms of ALS.
|
|
| 6. |
- Edvardsen, Hege, et al.
(author)
-
SNP in TXNRD2 Associated With Radiation-Induced Fibrosis : A Study of Genetic Variation in Reactive Oxygen Species Metabolism and Signaling.
- 2013
-
In: International journal of radiation oncology, biology, physics. - : Elsevier BV. - 1879-355X .- 0360-3016. ; 86:4, s. 791-9
-
Journal article (peer-reviewed)abstract
- PURPOSE: The aim of the study was to identify noninvasive markers of treatment-induced side effects. Reactive oxygen species (ROS) are generated after irradiation, and genetic variation in genes related to ROS metabolism might influence the level of radiation-induced adverse effects (AEs).METHODS AND MATERIALS: 92 breast cancer (BC) survivors previously treated with hypofractionated radiation therapy were assessed for the AEs subcutaneous atrophy and fibrosis, costal fractures, lung fibrosis, pleural thickening, and telangiectasias (median follow-up time 17.1 years). Single-nucleotide polymorphisms (SNPs) in 203 genes were analyzed for association to AE grade. SNPs associated with subcutaneous fibrosis were validated in an independent BC survivor material (n=283). The influence of the studied genetic variation on messenger ribonucleic acid (mRNA) expression level of 18 genes previously associated with fibrosis was assessed in fibroblast cell lines from BC patients.RESULTS: Subcutaneous fibrosis and atrophy had the highest correlation (r=0.76) of all assessed AEs. The nonsynonymous SNP rs1139793 in TXNRD2 was associated with grade of subcutaneous fibrosis, the reference T-allele being more prevalent in the group experiencing severe levels of fibrosis. This was confirmed in another sample cohort of 283 BC survivors, and rs1139793 was found significantly associated with mRNA expression level of TXNRD2 in blood. Genetic variation in 24 ROS-related genes, including EGFR, CENPE, APEX1, and GSTP1, was associated with mRNA expression of 14 genes previously linked to fibrosis (P≤.005).CONCLUSION: Development of subcutaneous fibrosis can be associated with genetic variation in the mitochondrial enzyme TXNRD2, critically involved in removal of ROS, and maintenance of the intracellular redox balance.
|
|
| 7. |
- Gong, Hanmo, et al.
(author)
-
Gold nanoparticle transfer through photothermal effects in a metamaterial absorber by nanosecond laser
- 2014
-
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4, s. 6080-
-
Journal article (peer-reviewed)abstract
- A non-complicated, controllable method of metallic nanoparticle fabrication at low operating light power is proposed. The method is based on laser-induced forward transfer, using a metamaterial absorber as the donor to significantly enhance the photothermal effect and reduce the operating light fluence to 35 mJ/cm(2), which is much lower than that in previous works. A large number of metallic nanoparticles can be transferred by one shot of focused nanosecond laser pulses. Transferred nanoparticles exhibit good size uniformity and the sizes are controllable. The optical properties of transferred particles are characterized by dark-field spectroscopy and the experimental results agree with the simulation results.
|
|
| 8. |
- Han, Yang, et al.
(author)
-
X-radiation inhibits histone deacetylase 1 and 2, upregulates Axin expression and induces apoptosis in non-small cell lung cancer
- 2012
-
In: Radiation Oncology. - : BioMed Central. - 1748-717X. ; 7:183
-
Journal article (peer-reviewed)abstract
- BackgroundHistone deacetylase (HDAC) plays an important role in the deacetylation of histone, which can alter gene expression patterns and affect cell behavior associated with malignant transformation. The aims of this study were to investigate the relationships between HDAC1, HDAC2, clinicopathologic characteristics, patient prognosis and apoptosis, to clarify the mechanism of upregulation of the Axis inhibitor Axin (an important regulator of the Wnt pathway) by X-radiation and to elucidate the effect of siRNA on radiation therapy of non-small cell lung cancer (NSCLC).MethodsHDAC1 and HDAC2 expression levels were measured by immunohistochemistry and reverse transcription PCR. Apoptosis was determined by terminal deoxynucleotidyl transferase-mediated dUTP-nick end labeling and fluorescence activated cell sorting. BE1 cells expressing Axin were exposed to 2 Gy of X-radiation.ResultsExpression of HDAC1 and that of HDAC2 were correlated, and significantly higher in NSCLC tissues than in normal lung tissues (P < 0.05). HDAC1 and HDAC2 expression was correlated with pTNM stage and negatively correlated with differentiation of NSCLC and apoptotic index (P < 0.05). The prognosis of patients with low expression of HDAC1 and HDAC2 was better than that of those with high expression. X-radiation and siRNA inhibited HDAC1 and HDAC2 expression in NSCLC cells and Axin levels were significantly higher in BE1 cells.ConclusionsX-radiation and siRNA inhibit expression of HDAC1 and HDAC2, weaken the inhibitory effect of HDAC on Axin, upregulate Axin expression and induce apoptosis of lung cancer cells. Inhibition of HDAC1 and HDAC2 is a means of enhancing the radiosensitivity of NSCLC.
|
|
| 9. |
- Qiu, Min, et al.
(author)
-
Nanostructured plasmonic devices and their applications
- 2013
-
In: 2013 IEEE 6th International Conference on Advanced Infocomm Technology, ICAIT 2013. - : IEEE. - 9781479904655 ; , s. 79-80
-
Conference paper (peer-reviewed)abstract
- In this talk, we will review our recent works on nanostructured plasmonic devices, and their applications in high performance light absorption, photothermal effects, and partly in photonic integrations.
|
|
| 10. |
- Qiu, Min, et al.
(author)
-
Plasmonic enhanced photothermal effects and its applications
- 2014
-
Conference paper (peer-reviewed)abstract
- We review here our recent studies on plasmonic enhanced photothermal effects in metallic nanostructure, and the applications of such effects. When light is shined on a prefect metamaterial absorber patterned with e-beam lithography, the gold nanoparticles (NPs) forming the absorber can be either transformed to nano-spherical-domes, or to truncated-octahedral shaped or multi-twined nanocrystals with large crystal grain sizes and flat boundary facets. The evolution of morphology and crystallinity of the gold NPs can be also observed. Evidences clearly show that the surface melting and the coalescence mechanism play a key role on nanocrystals formation. These melted gold nanospheres can even be transferred to another substrate, on which the transferred NPs exhibit excellent size uniformity. The strong photothermal effects can also be utilized to tune silicon photonics waveguides and resonators. It is shown that all-optical photothermal switching of Mach-Zehnder interferometers (MZI), silicon disk resonators, and silicon ring resonators is possible with the help of plasmonic nanoheaters. The switching response time and power consumption are all at reasonably low level.
|
|
