| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)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. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 3. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 4. |
- Yang, Xu-Fang, et al.
(författare)
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High efficient isolation and systematic identification of human adipose-derived mesenchymal stem cells
- 2011
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Ingår i: Journal of Biomedical Science. - : Springer Science and Business Media LLC. - 1021-7770 .- 1423-0127. ; 18, s. 59-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Developing efficient methods to isolate and identify human adipose-derived mesenchymal stem cells (hADSCs) remains to be one of the major challenges in tissue engineering. Methods: We demonstrate here a method by isolating hADSCs from abdominal subcutaneous adipose tissue harvested during caesarian section. The hADSCs were isolated from human adipose tissue by collagenase digestion and adherence to flasks. Results: The yield reached around 1 x 10(6) hADSCs per gram adipose tissue. The following comprehensive identification and characterization illustrated pronounced features of mesenchymal stem cells (MSCs). The fibroblast-like hADSCs exhibited typical ultrastructure details for vigorous cell activities. Karyotype mapping showed normal human chromosome. With unique immunophenotypes they were positive for CD29, CD44, CD73, CD105 and CD166, but negative for CD31, CD34, CD45 and HLA-DR. The growth curve and cell cycle analysis revealed high capability for self-renewal and proliferation. Moreover, these cells could be functionally induced into adipocytes, osteoblasts, and endothelial cells in the presence of appropriate conditioned media. Conclusion: The data presented here suggest that we have developed high efficient isolation and cultivation methods with a systematic strategy for identification and characterization of hADSCs. These techniques will be able to provide safe and stable seeding cells for research and clinical application.
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| 5. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 6. |
- Li, Jian-Fang, et al.
(författare)
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Soy isoflavone delays the progression of thioacetamide-induced liver fibrosis in rats
- 2011
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Ingår i: Scandinavian Journal of Gastroenterology. - : Informa UK Limited. - 1502-7708 .- 0036-5521. ; 46:3, s. 341-349
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Tidskriftsartikel (refereegranskat)abstract
- Objective. Our aim was to investigate the effect of soy isoflavone (SI) on liver fibrosis in a thioacetamide (TAA)-induced rat model. Materials and methods. Twenty-eight rats were assigned to four groups: sham group, fibrosis group, low-dose treatment group (LDg) and high-dose treatment group (HDg). SI (90 or 270 mg/kg) was administered daily during the model development by TAA. Standard liver tests, platelet derived growth factor-BB (PDGF-BB) and tissue inhibitor of metalloproteinase-1 (TIMP-1) were measured. The expression of collagen, alpha alpha-smooth muscle actin (alpha alpha-SMA) and transforming growth factor-beta beta 1 (TGF-beta beta 1) in liver tissue was determined. Electron microscopy was used to perform ultrastructural analysis of the livers. Results. Hepatic fibrosis was induced by 8 weeks of TAA administration. However, following the administration of SI, collagen staining significantly declined as compared with the fibrosis group (p < 0.01). Less collagen fibers around the hepatic stellate cells (HSCs) were observed in HDg as compared to the fibrosis group and LDg. There was no significant difference in standard liver tests between the fibrosis group and the two treatment groups. The levels of PDGF-BB and TIMP-1 in the two SI-treated groups were significantly lower than in the fibrosis group (p < 0.01). The expression of alpha alpha-SMA and TGF-beta beta 1 in HDg was less than that in the fibrosis group and LDg (p < 0.01). Conclusion. Administration of a high dose of SI resulted in an obvious inhibitory effect on liver fibrosis induced by TAA in rats. One hypothesis is that the effect may be related to the inhibition of HSC activation and proliferation.
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| 7. |
- Du, Fang K., et al.
(författare)
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Direction and extent of organelle DNA introgression between two spruce species in the Qinghai-Tibetan Plateau
- 2011
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 192:4, s. 1024-1033
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Tidskriftsartikel (refereegranskat)abstract
- A recent model has shown that, during range expansion of one species in a territory already occupied by a related species, introgression should take place preferentially from the resident species towards the invading species and genome components experiencing low rates of gene flow should introgress more readily than those experiencing high rates of gene flow. Here, we use molecular markers from two organelle genomes with contrasted rates of gene flow to test these predictions by examining genetic exchanges between two morphologically distinct spruce Picea species growing in the Qinghai-Tibetan Plateau. The haplotypes from both mitochondrial (mt) DNA and chloroplast (cp) DNA cluster into two distinct lineages that differentiate allopatric populations of the two species. By contrast, in sympatry, the species share the same haplotypes, suggesting interspecific genetic exchanges. As predicted by the neutral model, all sympatric populations of the expanding species had received their maternally inherited mtDNA from the resident species, whereas for paternally inherited cpDNA introgression is more limited and not strictly unidirectional. Our results underscore cryptic introgressions of organelle DNAs in plants and the importance of considering rates of gene flow and range shifts to predict direction and extent of interspecific genetic exchanges.
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| 8. |
- Hu, Jing, et al.
(författare)
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Hydrothermal preparation of boehmite-doped AgCl nanocubes and their characterization
- 2011
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Ingår i: Materials letters (General ed.). - : Elsevier BV. - 0167-577X .- 1873-4979. ; 65:11, s. 1531-1534
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Tidskriftsartikel (refereegranskat)abstract
- A simple hydrothermal route to the preparation of the boehmite-doped AgCl nanocubes using AgNO3,AlCl3 center dot 6H(2)O and NaOH at 200 degrees C for 24 h is reported. The products were characterized by X-ray powder diffraction (XRD), Fourier transform infrared spectrometry (FT-IR), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), selected area electron diffraction (SAED), UV-vis, thermogravimetric analysis (TGA), and differential thermal analysis (DTA). FE-SEM and TEM micrographs showed that the obtained boehmite-doped AgCl had nanocube-like morphology. The influence of heating temperature on the phase, microstructure, morphology, and thermal stability of the products were also investigated. UV-visible results indicated that the absorption edge moved to higher wavelength with the increasing heating temperature. These materials would be a promising material for photocatalyst applications.
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| 9. |
- Li-Juan, Zhang, et al.
(författare)
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A novel water layer structure inside nanobubbles at room temperature
- 2014
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Ingår i: NUCL SCI TECH. - 1001-8042. ; 25:6, s. 060503-
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Tidskriftsartikel (refereegranskat)abstract
- Molecularly thin water layer, with a hydrogen bonding network different from those in bulk water and ice, has unique properties and is generally involved in many important processes such as wetting, erosion, atmosphere chemical reaction, protein folding and biomolecular interaction. Here, we report a new water layer structure at room temperature, which is found inside nanobubbles by using synchrotron based scanning transmission soft X-ray microscopy (STXM). The three peaks 535.0, 536.8 and 540.9 eV at O K edge inside the nanobubbles show a novel characteristics of very thin water layers, which has never been observed before.
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| 10. |
- Ma, Tao, et al.
(författare)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Tidskriftsartikel (refereegranskat)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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| 11. |
- Wu, Jing-Fang, et al.
(författare)
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Extracranial and intracranial complications of otitis media : 22-year clinical experience and analysis
- 2012
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Ingår i: Acta Oto-Laryngologica. - : Informa UK Limited. - 0001-6489 .- 1651-2251. ; 132:3, s. 261-265
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Tidskriftsartikel (refereegranskat)abstract
- Conclusion: The morbidity of the complications has had a decreased tendency in recent decades, but the category of the complications was rather diverse. There are still many serious complications that require our attention. Surgery is still the most important treatment option. Objective: To investigate otogenic extracranial and intracranial complications in patients with acute and chronic otitis media. Methods: A retrospective study investigated 285 patients with extracranial and intracranial complications among the 2346 inpatients with acute or chronic otitis media with or without cholesteatoma admitted to the Department of Otolaryngology, AnHui Medical University Hospital between 1987 and 2008. Results: In the 285 patients with cranial complications, 253 had a single complication, 29 had two complications, and 3 had more than two complications. Intracranial complications included meningitis (16 cases), brain abscess (42 cases), sigmoid sinus involvement (29 cases), extradural abscess (8 cases), subdural abscess (1 case), and hydrocephalus (2 cases). Extracranial complications included labyrinthitis (90 cases), mastoid abscess (79 cases), facial paralysis (47 cases), Bezold abscess (5 cases), and apicitis pyramidalis (1 case). In all, 267 patients were cured or improved without recurrence. Five patients died from complications, of whom four died of cerebral hernia and one died of multiple abscesses.
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