| 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. |
- Teng, Chao, et al.
(author)
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Molecular Design of Anthracene-Bridged Metal-Free Organic Dyes for Efficient Dye-Sensitized Solar Cells
- 2010
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:19, s. 9101-9110
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Journal article (peer-reviewed)abstract
- A series of metal-free organic dyes bridged by anthracene-containing pi-conjugations were designed and synthesized as new chromophores for the application of dye-sensitized solar cells (DSCs). Detailed investigations on the relationship between the dye structures, photophysical properties, electrochemical properties, and performances of DSCs are described. With the introduction of the anthracene moiety, together with a triple bond for the fine-tuning of molecular planar configurations and to broaden absorption spectra, the short-circuit photocurrent densities (J(sc)) and open-circuit photovoltages (V-oc) of DSCs were improved to a large extent. The improvement of J(sc) is attributed to much broader absorption spectra of the dyes with the anthracene moiety. Electrochemical impedance spectroscopy (EIS) analysis reveals that the introduction of the anthracene moiety suppresses the charge recombination arising from electrons in TiO2 films with I-3(-) ions in the electrolyte, thus improving V-oc considerably. On the basis of optimized molecular structures and DSC test conditions, the dye TC501 shows a prominent solar energy conversion efficiency (eta) up to 7.03% (J(sc) = 12.96 mA . cm(-2), V-OC = 720 mV, ff = 0.753) under simulated AM 1.5 irradiation (100 mW . cm(-2)).
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| 3. |
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| 4. |
- Chen, Chao, et al.
(author)
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Effects of Salt Tracer Amount, Concentration and Kind on the Fluid Flow Behavior in a Hydrodynamic Model of Continuous Casting Tundish
- 2012
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In: Steel Research International. - : John Wiley & Sons. - 1611-3683 .- 1869-344X. ; 83:12, s. 1141-1151
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Journal article (peer-reviewed)abstract
- The hydrodynamic modeling method that widely used to simulate the fluid flow was reconsidered and discussed in this paper. The effects of injected salt tracer amount, concentration and kind on the fluid flow behavior in a hydrodynamic model tundish were investigated. The results were compared with the mathematical modeling calculation results, that the tracer density effect was eliminated. The residence time distribution (RTD) curve of tracer introduced deviated to the left side of the calculated curve, besides the deviation was increased as dimensionless tracer amount (the ratio of tracer amount to hydrodynamic model tundish volume) increased from 0.202 × 10−3 to 1.008 × 10−3. The results of tracer concentration study were similar, namely the deviation was increased with concentration increased; on the other hand, the deformation of a “stair-shape” RTD curve occurred when tracer concentration was much lower (at dimensionless tracer amount of 0.168 × 10−3 with converting to saturated solution). Besides, the effect of tracer kind on the accuracy of hydrodynamic modeling was also studied; the measurements of KCl solution with lower density than that of NaCl solution exhibited more of accuracy. Finally, the optimized tracer in hydrodynamic model tundish of present work is saturated KCl solution with dimensionless tracer amount of 0.202 × 10−3.
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| 5. |
- Cheng, Xiaoxiao, et al.
(author)
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Structure and Interactions of the Human Programmed Cell Death 1 Receptor
- 2013
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In: Journal of Biological Chemistry. - : American Society for Biochemistry and Molecular Biology. - 0021-9258 .- 1083-351X. ; 288:17, s. 11771-11785
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Journal article (peer-reviewed)abstract
- PD-1, a receptor expressed by T cells, B cells, and monocytes, is a potent regulator of immune responses and a promising therapeutic target. The structure and interactions of human PD-1 are, however, incompletely characterized. We present the solution nuclear magnetic resonance (NMR)-based structure of the human PD-1 extracellular region and detailed analyses of its interactions with its ligands, PD-L1 and PD-L2. PD-1 has typical immunoglobulin superfamily topology but differs at the edge of the GFCC' sheet, which is flexible and completely lacks a C '' strand. Changes in PD-1 backbone NMR signals induced by ligand binding suggest that, whereas binding is centered on the GFCC' sheet, PD-1 is engaged by its two ligands differently and in ways incompletely explained by crystal structures of mouse PD-1.ligand complexes. The affinities of these interactions and that of PD-L1 with the costimulatory protein B7-1, measured using surface plasmon resonance, are significantly weaker than expected. The 3-4-fold greater affinity of PD-L2 versus PD-L1 for human PD-1 is principally due to the 3-fold smaller dissociation rate for PD-L2 binding. Isothermal titration calorimetry revealed that the PD-1/PD-L1 interaction is entropically driven, whereas PD-1/PD-L2 binding has a large enthalpic component. Mathematical simulations based on the biophysical data and quantitative expression data suggest an unexpectedly limited contribution of PD-L2 to PD-1 ligation during interactions of activated T cells with antigen-presenting cells. These findings provide a rigorous structural and biophysical framework for interpreting the important functions of PD-1 and reveal that potent inhibitory signaling can be initiated by weakly interacting receptors.
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| 6. |
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| 7. |
- Negre, Nicolas, et al.
(author)
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A cis-regulatory map of the Drosophila genome
- 2011
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 471:7339, s. 527-531
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Journal article (peer-reviewed)abstract
- Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide(1,2) has successfully identified specific subtypes of regulatory elements(3). In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements(4), chromatin states(5), transcription factor binding sites(6-9), RNA polymerase II regulation(8) and insulator elements(10); however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.
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| 8. |
- Teng, Chao, et al.
(author)
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Tuning the HOMO Energy Levels of Organic Dyes for Dye-Sensitized Solar Cells Based on Br(-)/Br(3)(-) Electrolytes
- 2010
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In: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 16:44, s. 13127-13138
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Journal article (peer-reviewed)abstract
- A series of novel metal free organic dyes TC301-TC310 with relatively high HOMO levels were synthesized and applied in dye sensitized solar cells (DSCs) based on electrolytes that contain Br(-)/Br(3)- and I(-)/I(3)(-) The effects of additive Li(+) ions and the HOMO levels of the dyes have an important influence on properties of the dyes and performance of DSCs The addition of Li(+) ions in electrolytes can broaden the absorption spectra of the dyes on TiO(2) films and shift both the LUMO levels of the dyes and the conduction band of TiO(2) thus leading to the increase of J(sc) and the decrease of V(oc) Upon using Br(-)/Br(3)(-) instead of I(-)/I(3)(-), a large increase of V(oc) is attributed to the enlarged energy difference between the redox potentials of electrolyte and the Fermi level of TiO(2), as well as the suppressed electron recombination Incident photon to current efficiency (IPCE) action spectra, electrochemical impedance spectra, and nanosecond laser transient absorption reveal that both the electron collection yields and the dye regeneration yields ((sic)(r)) depend on the potential difference (the driving forces) between the oxidized dyes and the Br(-)/Br(3)(-) redox couple For the dyes for which the HOMO levels are more positive than the redox potential of Br(-)/Br(3)(-) sufficient driving forces lead to the longer effective electron diffusion lengths and almost the same efficient dye regenerations, whereas for the dyes for which the HOMO levels are similar to the redox potential of Br(-)/Br(3)(-), insufficient driving forces lead to shorter effective electron-diffusion lengths and inefficient dye regenerations
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| 9. |
- Xu, Peng, et al.
(author)
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Ultra-shallow junctions formed using microwave annealing
- 2013
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In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 102:12, s. 122114-
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Journal article (peer-reviewed)abstract
- Microwave annealing is shown to be viable for achieving low thermal budget formation of ultra-shallow junctions. Regrowth of a 10 nm thick amorphous Si layer that is generated during a Ge amorphization process prior to BF2 or As dopant implantation proceeds at rates up to 0.53 nm/min for BF2 and up to 0.33 nm/min for As at 370 degrees C. The fraction of electrical activation for implanted dopants is as high as 13% for BF2 and 32% for As with negligible diffusion at 540 degrees C.
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| 10. |
- Zhang, Lun, et al.
(author)
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Reconstruction of defects following surgery for hypopharyngeal carcinoma using artificial biological material
- 2010
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In: Acta Oto-Laryngologica. - : Informa UK Limited. - 0001-6489 .- 1651-2251. ; 130:11, s. 1293-1299
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Journal article (peer-reviewed)abstract
- Conclusions: Use of artificial biological material - acellular dermal matrix (Alloderm, ADM) - combined with pectoralis major myocutaneous flaps (PMMFs) or other cervical tissue is a feasible technique with which to reconstruct a large circumferential defect involving the oral cavity and hypopharynx. Objective: This paper presents a review of seven patients with advanced hypopharyngeal carcinoma treated at Tianjin Medical University Cancer Institute & Hospital, China, over a 4-year period. Methods: ADM was used in the form of tissue patches for reconstruction. Five of the seven patients underwent total laryngectomy and total hypopharyngectomy, and reconstruction with a combination of PMMF and ADM tissue patches to restore hypopharyngeal functions. Two other patients underwent tumour resection. The defect in the posterior pharyngeal wall was reconstructed with ADM. Treatment details of the seven patients are discussed. Results: All five PMMFs and seven ADM tissue patches survived. No pharyngeal fistula occurred. Satisfactory healing was observed between the wound margin and ADM 10 days after operation. The trauma area was completely covered by growing epithelium 18-37 days after operation. To some degree, stenosis of the pharyngeal cavity did occur, but patients could have a regular diet following dilatation of the stenosis. Five patients are free of disease after 18-42 months of follow-up.
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