| 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. |
- Li, Wei, et al.
(author)
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Variation in floral phenological synchronization in a clonal seed orchard of pinus tabuliformis in northeast of China
- 2012
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In: Silvae Genetica. - 0037-5349. ; 61:4-5, s. 133-142
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Journal article (peer-reviewed)abstract
- Flowering phenology in an orchard is a crucial factor affecting the gene exchange among clones and consequently changing genetic composition of the seed crop. Pinus tabuliformis is now at the crucial period from first generation clonal seed orchards to advanced generation seed orchards in China. In this study, variation and stability in floral phenological synchronization of all the clones and possible mating pairs, in terms of an index of phenological overlap, were observed in a first generation clonal seed orchard which located in northeast of China. Results showed that significant variations occurred in the clones and mating pairs. This kind of variation was apparently related with temperature and humidity of the research site. With increasing age, levels of flowering synchronization were likely to rise in the clones and mating pairs. In general, the average flowering synchronization of male parents was slightly higher than that of female parents, female management in a seed orchard should be paied more attention. Flowering time was under strong genetic control and this genetic control was stronger in the female flowering process than of the males in terms of board sense heritability and year to year correlation analysis. Flowering synchronization of female parents was positively correlated between most years and can be a reliable reference for early and late predication in Pinus tabuliformis seed orchard during stage of initial seed harvest to stable seed production. According to their average levels of flowering synchronization, 49 clones in the first generation clonal seed orchard were divided into 11 different groups. Results of this paper provided the basic information for first generation seed orchard management and advanced seed orchard establishment of Pinus tabuliformis.
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| 3. |
- Zhao, Zeng-Ren, et al.
(author)
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Significance of mRNA and Protein Expression of MAC30 in Progression of Colorectal Cancer
- 2011
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In: Chemotherapy. - Basel : Karger AG. - 0009-3157 .- 1421-9794. ; 57:5, s. 394-401
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Journal article (peer-reviewed)abstract
- Background: Meningioma-associated protein (MAC30), first described to be overexpressed in meningiomas, exhibits altered expression in certain human tumors. The aim of our study was to investigate the expression of MAC30 mRNA and its correlation with clinicopathological variables in human colorectal cancer (CRC). Methods: MAC30 mRNA expression was first examined in 55 CRCs, along with the samples from the matched distant normal and adjacent noncancerous tissue by RT-PCR, further verified in 18 CRCs by quantitative RT-PCR. MAC30 protein expression was detected by Western blot in 10 CRCs, and DNA sequencing was performed in 1 case of the paired CRC and the matched noncancerous specimen. MAC30 mRNA expression in two colon cancer cell lines, HCT-116(p53-/-) and HCT-116(p53+/+), was detected by quantitative RT-PCR. Results: The mRNA expression of MAC30 was increased in CRC when compared with distant normal (p < 0.01) and adjacent noncancerous mucosa (p < 0.01). The mean value of MAC30 mRNA expression in the tumor located in the colon was higher than in the rectum (0.677 +/- 0.419 vs. 0.412 +/- 0.162, p = 0.005). As the tumor penetrated the wall of the colon/rectum, MAC30 mRNA expression notably increased in tumors with T3+T4 stage compared to tumors with T1+T2 stage (0.571 +/- 0.364 vs. 0.404 +/- 0.115, p = 0.014). MAC30 protein expression in CRCs was also remarkably elevated compared to the adjacent noncancerous mucosa. There was no mutation in the coding region of the MAC30 gene either in CRC or in the noncancerous mucosa. mRNA expression of p53 was notably decreased in HCT-116(p53-/-) compared to HCT-116(p53+/+), while MAC30 did not vary greatly. Conclusion: The overexpression of MAC30 might be involved in the development and aggressiveness of CRCs, especially in the colon.
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| 4. |
- Du, Yaoyao, et al.
(author)
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Cartilage Oligomeric Matrix Protein Inhibits Vascular Smooth Muscle Calcification by Interacting With Bone Morphogenetic Protein-2.
- 2011
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In: Circulation Research. - 1524-4571. ; 108, s. 79-917
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Journal article (peer-reviewed)abstract
- Rationale: Vascular calcification is a significant contributor to cardiovascular morbidity and mortality. We recently reported that cartilage oligomeric matrix protein (COMP) is pivotal for maintaining the homeostasis of vascular smooth muscle cells (VSMCs). Whether COMP affects the process of vascular calcification is unknown. Objective: We aimed to test whether COMP modulates vascular calcification. Methods and Results: VSMC calcification in vitro was induced by calcifying media containing high inorganic phosphate or calcium. In vivo medial vessel calcification was induced in rats by 5/6 nephrectomy with a high-phosphate diet or by periadventitial application of CaCl(2) to the abdominal aorta. COMP protein level was markedly reduced in both calcified VSMCs and arteries. COMP deficiency remarkably exacerbated VSMC calcification, whereas ectopic expression of COMP greatly reduced calcification. Furthermore, COMP knockdown facilitated osteogenic markers expression by VSMCs even in the absence of calcifying media. By contrast, COMP overexpression significantly inhibited high phosphate- or high calcium-induced VSMC osteochondrogenic transition. Induction of osteogenic marker expression by COMP silencing was reversed by a soluble form of bone morphogenetic protein (BMP)-2 receptor IA, which suggests a BMP-2-dependent mechanism. Our data revealed that COMP bound directly to BMP-2 through the C terminus, inhibited BMP-2 receptor binding, and blocked BMP-2 osteogenic signaling, indicating COMP inhibits osteochondrogenic transition of VSMCs at least partially through inhibiting BMP-2. Conclusions: Our data strongly suggest that COMP is a novel inhibitor of vascular calcification. The imbalance between the effects of COMP and BMP-2 may provide new insights into the pathophysiology of vascular calcification.
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| 5. |
- Ge, Yue, et al.
(author)
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Environmental OMICS: Current Status and Future Directions
- 2013
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In: JOURNAL OF INTEGRATED OMICS. - : Proteomass Scientific Society. - 2182-0287. ; 3:2, s. 75-87
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Journal article (peer-reviewed)abstract
- Applications of OMICS to high throughput studies of changes of genes, RNAs, proteins, metabolites, and their associated functionsin cells or organisms exposed to environmental chemicals has led to the emergence of a very active research field: environmental OMICS.This developing field holds an important key for improving the scientific basis for understanding the potential impacts of environmentalchemicals on both health and the environment. Here we describe the state of environmental OMICS with an emphasis on its recent accomplishmentsand its problems and potential solutions to facilitate the incorporation of OMICS into mainstream environmental and healthresearch.Data sources: We reviewed relevant and recently published studies on the applicability and usefulness of OMICS technologies to the identificationof toxicity pathways, mechanisms, and biomarkers of environmental chemicals for environmental and health risk monitoring andassessment, including recent presentations and discussions on these issues at The First International Conference on Environmental OMICS(ICEO), held in Guangzhou, China during November 8-12, 2011. This paper summarizes our review.Synthesis: Environmental OMICS aims to take advantage of powerful genomics, transcriptomics, proteomics, and metabolomics tools toidentify novel toxicity pathways/signatures/biomarkers so as to better understand toxicity mechanisms/modes of action, to identify/categorize/prioritize/screen environmental chemicals, and to monitor and predict the risks associated with exposure to environmental chemicalson human health and the environment. To improve the field, some lessons learned from previous studies need to be summarized, aresearch agenda and guidelines for future studies need to be established, and a focus for the field needs to be developed.Conclusions: OMICS technologies for identification of RNA, protein, and metabolic profiles and endpoints have already significantly improvedour understanding of how environmental chemicals affect our ecosystem and human health. OMICS breakthroughs are empoweringthe fields of environmental toxicology, chemical toxicity characterization, and health risk assessment. However, environmental OMICS is stillin the data generation and collection stage. Important data gaps in linking and/or integrating toxicity data with OMICS endpoints/profilesneed to be filled to enable understanding of the potential impacts of chemicals on human health and the environment. It is expected thatfuture environmental OMICS will focus more on real environmental issues and challenges such as the characterization of chemical mixturetoxicity, the identification of environmental and health biomarkers, and the development of innovative environmental OMICS approachesand assays. These innovative approaches and assays will inform chemical toxicity testing and prediction, ecological and health risk monitoringand assessment, and natural resource utilization in ways that maintain human health and protects the environment in a sustainable manner.
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| 6. |
- Hua, Weijie, et al.
(author)
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X-ray spectroscopy of blocked alanine in water solution from supermolecular and supermolecular-continuum solvation models : a first-principles study
- 2012
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 14:27, s. 9666-9675
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Journal article (peer-reviewed)abstract
- The N1s near-edge X-ray absorption fine structure (NEXAFS) and X-ray emission spectra (XES) of blocked alanine in water solution have been investigated at the first-principles level based on cluster models constructed from classical molecular dynamics simulations. The bulk solvent has been described by both supermolecular and combined supermolecular-continuum models. With the former model we show that NEXAFS spectra convergent with respect to system size require at least the inclusion of the second solvation shell and that averaged spectra over several hundreds of snapshots can well represent the statistical effect of different instantaneous configurations of the solvation shells. With the combined model we demonstrate that calculations of a medium-sized peptide-water supermolecule qualitatively predict the NEXAFS spectrum of the solvated peptide even considering a single geometry. Furthermore, sampling over hundreds of snapshots by the combined model, the explicit inclusion of even a few waters yields an averaged spectrum in good quantitative agreement with the discrete model results. In comparison, the XES spectra show little dependence on the structures
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| 7. |
- Ma, Tao, et al.
(author)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Journal article (peer-reviewed)abstract
- Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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| 8. |
- Shahid, Naeem, et al.
(author)
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Novel postetch process to realize high quality photonic crystals in InP
- 2011
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In: Journal of Vacuum Science & Technology B. - : American Vacuum Society. - 1071-1023 .- 1520-8567. ; 29:3, s. 031202-
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Journal article (peer-reviewed)abstract
- Thermally driven reflow of material during annealing was positively used to obtain near-vertical sidewall profiles for high-aspect-ratio nanostructures in InP fabricated by dry etching. This is very promising for achieving high optical quality in photonic crystal (PhC) components. Nearly cylindrical profiles were obtained for high-aspect-ratio PhC holes with diameters as small as 200350 nm. Mini stop bands (MSBs) in line-defect PhC waveguides were experimentally investigated for both as-etched and reshaped hole geometries, and their spectral characteristics were used to assess the quality of PhC fabrication. The spectral characteristics of the MSB in PhC waveguides with reshaped holes showed significant improvement in performance with a transmission dip as deep as 35 dB with sharp edges dropping in intensity more than 30 dB for similar to 4 nm of wavelength change. These results show potential for using high extinction drop-filters in InP-based monolithic photonic integrated circuit applications. Finally, it is proposed that other nanostructure geometries may also benefit from this reshaping process.
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| 9. |
- Shen, Yue, 1981-, et al.
(author)
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Plasminogen initiates and potentiates the healing of acute and chronic tympanic membrane perforations in mice
- 2014
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In: Journal of Translational Medicine. - : BioMed Central. - 1479-5876. ; 12
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Journal article (peer-reviewed)abstract
- Background: Most tympanic membrane (TM) perforations heal spontaneously, but approximately 10-20% remain open as chronic TM perforations. Chronic perforations can lead to an impaired hearing ability and recurrent middle ear infections. Traditionally, these perforations must be surgically closed, which is costly and time consuming. Therefore, there is a need for simpler therapeutic strategies. Previous studies by us have shown that plasminogen (plg) is a potent pro-inflammatory regulator that accelerates cutaneous wound healing in mice. We have also shown that the healing of TM perforations is completely arrested in plg-deficient (plg(-/-)) mice and that these mice develop chronic TM perforations. In the present study, we investigated the therapeutic potential of local plg injection in acute and chronic TM perforation mice models. Methods: Plg(-/-) mice and wild-type mice were subjected to standardized TM perforations followed by local injection of plg into the soft tissue surrounding the TM. TM perforations with chronic characteristics were induced by leaving TM perforations in plg(-/-) mice untreated for 9 days before treatment. The healing process was observed through otomicroscope and finally confirmed by immunostaining. The quality of TM healing was evaluated based on the morphology of the TM. Result: Daily local injections of plg into the soft tissue surrounding the TM restored the ability to heal TM perforations in plg(-/-) mice in a dose-dependent manner, and potentiated the healing rate and quality in wild-type mice. A single local injection of plg initiated the healing of the chronic-like TM perforations in these mice, resulting in a closed TM with a continuous but rather thick outer keratinocyte layer. However, three plg injections led to a completely healed TM with a thin keratinizing squamous epithelium covering a connective tissue layer. Conclusion: Our data suggests that plg is a promising drug candidate for the treatment of chronic TM perforations in humans.
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| 10. |
- Shen, Yue, et al.
(author)
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Plasminogen is a key proinflammatory regulator that accelerates the healing of acute and diabetic wounds
- 2012
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In: Blood. - Washington, USA : American society of hematology. - 0006-4971 .- 1528-0020. ; 119:24, s. 5879-5887
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Journal article (peer-reviewed)abstract
- Despite decades of research on wound healing, effective biologic agents for the treatment of chronic wounds, especially diabetic wounds, are still lacking. In the present study, we report that the inert plasma protein plasminogen (plg) acts as a key regulatory molecule that potentiates wound healing in mice. Early in the healing process, plg bound to inflammatory cells is transported to the wound area, where the level of plg is increased locally, leading to the induction of cytokines and intracellular signaling events and to a potentiation of the early inflammatory response. Systemic administration of additional plg not only accelerates the healing of acute burn wounds in wild-type mice, but also improves the healing of chronic diabetic wounds in a mouse model of diabetes. Our results suggest that the administration of plg may be a novel therapeutic strategy to treat many different types of wounds, especially chronic wounds such as those caused by diabetes. (Blood. 2012; 119(24):5879-5887)
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