| 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. |
- Alfirevic, A., et al.
(författare)
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Phenotype Standardization for Statin-Induced Myotoxicity
- 2014
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Ingår i: Clinical Pharmacology and Therapeutics. - : Springer Science and Business Media LLC. - 0009-9236 .- 1532-6535. ; 96:4, s. 470-476
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Forskningsöversikt (refereegranskat)abstract
- Statins are widely used lipid-lowering drugs that are effective in reducing cardiovascular disease risk. Although they are generally well tolerated, they can cause muscle toxicity, which can lead to severe rhabdomyolysis. Research in this area has been hampered to some extent by the lack of standardized nomenclature and phenotypic definitions. We have used numerical and descriptive classifications and developed an algorithm to define statin-related myotoxicity phenotypes, including myalgia, myopathy, rhabdomyolysis, and necrotizing autoimmune myopathy.
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| 3. |
- Wadelius, Mia, et al.
(författare)
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Phenotype Standardization of Angioedema in the Head and Neck Region Caused by Agents Acting on the Angiotensin System
- 2014
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Ingår i: Clinical Pharmacology and Therapeutics. - : Nature Publishing Group. - 0009-9236 .- 1532-6535. ; 96:4, s. 477-481
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Forskningsöversikt (refereegranskat)abstract
- Angioedema is a potentially life-threatening adverse reaction to angiotensin-converting enzyme inhibitors and angiotensin receptor blockers. To study the genetic etiology of this rare adverse event, international consortia and multicenter recruitment of patients are needed. To reduce patient heterogeneity, we have standardized the phenotype. In brief, it comprises swelling in the head and neck region that first occurs during treatment. It should not coincide with urticaria or have another likely cause such as hereditary angioedema.
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| 4. |
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| 5. |
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| 6. |
- Hugerth, Luisa W., et al.
(författare)
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Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:4, s. 095567-
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired-or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems.
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| 7. |
- Kushnir, Mark M., et al.
(författare)
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Liquid chromatography tandem mass spectrometry for analysis of steroids in clinical laboratories
- 2011
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Ingår i: Clinical Biochemistry. - : Elsevier BV. - 0009-9120 .- 1873-2933. ; 44:1, s. 77-88
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Forskningsöversikt (refereegranskat)abstract
- Liquid chromatography tandem mass spectrometry is one of the most specific techniques available in clinical laboratories. In the past, immunoassays were the primary methodology for analysis of steroids in biological samples because they are rapid and easy to perform. However, these methods were shown to suffer from the lack of specificity for measuring many of the diagnostically important steroids. LC-MS/MS overcomes many of the limitations of immunoassays, enhances diagnostic utility of the testing, and expands diagnostic capabilities in endocrinology. In addition to the superior quality of the measurements, LC-MS/MS allows high throughput testing using small sample volume with minimal sample preparation, and frees the laboratory from dependence on suppliers of assay specific reagents. LC-MS/MS is being widely employed for routine measurement of steroids, and the methodology plays an important role in the standardization and harmonization of measurements among clinical laboratories.
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| 8. |
- 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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| 9. |
- O'Hurley, Gillian, et al.
(författare)
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Investigation of molecular alterations of AKT-3 in triple-negative breast cancer
- 2014
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Ingår i: Histopathology. - : Wiley. - 0309-0167 .- 1365-2559. ; 64:5, s. 660-670
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Tidskriftsartikel (refereegranskat)abstract
- Aims Triple-negative breast cancer (TNBC) is responsible for a disproportionate number of breast cancer (BC) deaths, owing to its intrinsic aggressiveness and a lack of treatment options, especially targeted therapies. Thus, there is an urgent need for the development of better targeted treatments for TNBC. Molecular alteration of AKT-3 was previously reported in oestrogen receptor (ER)-positive BC. AKT-3 has also been suggested to play a role in hormone-unresponsive BC. The aim of this study was to investigate molecular alterations of AKT-3 in TNBC, to perform associated survival analysis, and to compare these findings with the incidence of AKT-3 molecular alterations in ER-positive BC. Results Our study revealed AKT-3 amplification and deletions in 11% (9/82) and 13% (11/82) of TNBCs, respectively. In contrast, 1% (2/209) of ER-positive BCs were found to have AKT-3 amplifications and deletions. A higher prevalence of AKT-3 copy number gains was observed in TNBC [26% (21/82)] than in ER-positive BC [9% (19/209)]. AKT-3 amplification together with Akt-3 protein expression was negatively associated with recurrence-free survival in TNBC. Furthermore, a negative association between high AKT-3 copy number and recurrence-free survival was observed. Conclusion AKT-3 amplification could represent a potentially relevant oncogenic event in a subset of TNBCs that may, in turn, select cells sensitive to Akt-3 inhibitors.
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| 10. |
- Tang, Yue, et al.
(författare)
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A comparative study of the application of the standard kernel density estimation and network kernel density estimation in crash hotspot identification
- 2013
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Ingår i: Proceedings of the 16th International Conference Road Safety on Four Continents. - Linköping : Statens väg- och transportforskningsinstitut.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Despite a growing number of studies have claimed the network Kernel Density Estimation (network KDE) a more advanced method for crash hotspot identification than the planar Kernel Density Estimation (planar KDE), few conducted comprehensive study to examine their accuracy and practicality on a large-scale basis (i.e. municipal and county). This research attempted to fill the gap by conducting a comparative study of planar KDE and network KDE using the crash data of Hampden County, Massachusetts from 2009 to 2011. A two-tier planar KDE and a network KDE were implemented using the Kernel Density tool in ESRI ArcGIS 10 and SANET 4.1 developed at University of Tokyo respectively. Results showed that (1) Planar KDE is computationally inexpensive and easily accessed. (2) Both methods yielded virtually similar hotspot patterns but with different rankings of the high crash locations. (3) In identifying specific hotspot locations, network KDE could achieve more accurate results and was more timesaving, although multiple runs of planar KDE identified specific locations as well. Accordingly, several suggestions were made for crash hotspot analysis: (1) Since KDE takes the interrelationship among crashes into consideration, it is a more statistically sound approach than traditional methods in crash hotspot identification and can be widely adopted by state and local agencies for initiating safety improvement projects. (2) Planar KDE is recommended to identify general hotspot patterns on large-scale basis for its practicality and efficiency. (3) Network KDE is recommended to identify specific intersections and roadway segments for accuracy.
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| 11. |
- Wang, Z. B., et al.
(författare)
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Characteristics of regional new particle formation in urban and regional background environments in the North China Plain
- 2013
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Ingår i: Atmos. Chem. Phys.. - : Copernicus Publications. - 1680-7324. ; 13:24, s. 12495-12506
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Tidskriftsartikel (refereegranskat)abstract
- Long-term measurements of particle number size distributions were carried out both at an urban background site (Peking University, PKU) and a regional Global Atmospheric Watch station (Shangdianzi, SDZ) from March to November in 2008. In total, 52 new particle formation (NPF) events were observed simultaneously at both sites, indicating that this is a regional phenomenon in the North China Plain. On average, the mean condensation sink value before the nucleation events started was 0.025 s−1 in the urban environment, which was 1.6 times higher than that at regional site. However, higher particle formation and growth rates were observed at PKU (10.8 cm−3 s−1 and 5.2 nm h−1) compared with those at SDZ (4.9 cm−3 s−1 and 4.0 nm h−1). These results implied that precursors were much more abundant in the polluted urban environment. Different from the observations in cleaner environments, the background conditions of the observed particle homogeneous nucleation events in the North China Plain could be characterized as the co-existing of a stronger source of precursor gases and a higher condensational sink of pre-existing aerosol particles. Secondary aerosol formation following nucleation events results in an increase of particle mass concentration, particle light scattering coefficient, and cloud condensation nuclei (CCN) number concentration, with consequences on visibility, radiative effects, and air quality. Typical regional NPF events with significant particle nucleation rates and subsequent particle growth over a sufficiently long time period at both sites were chosen to investigate the influence of NPF on the number concentration of "potential" CCN. As a result, the NPF and the subsequent condensable growth increased the CCN number concentration in the North China Plain by factors in the range from 5.6 to 8.7. Moreover, the potential contribution of anthropogenic emissions to the CCN number concentration was more than 50%, to which more attention should be drawn in regional and global climate modeling, especially in the polluted urban areas.
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| 12. |
- Yang, Tien-Nan, et al.
(författare)
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Variations in monsoonal rainfall over the last 21 kyr inferred from sedimentary organic matter in Tung-Yuan Pond, southern Taiwan
- 2011
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Ingår i: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 30:23-24, s. 3413-3422
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Tidskriftsartikel (refereegranskat)abstract
- Changes in paleorainfall intensity linked to the strength of the East Asian (EA) summer monsoon since 21 cal kyr BP are inferred from the organic matter contents of a 15-m sediment core from Tung-Yuan Pond in southern Taiwan. High total organic carbon/total nitrogen (TOC/TN) values in association with increased TOC content suggest that more soil-derived material containing terrestrial organic matter (OM) was delivered to the lake during periods of increased runoff associated with extensive precipitation that resulted from intensified summer monsoons, whereas low values indicate OM possessing a dominant algal origin during weakened summer monsoons. Rainfall intensity in terms of the proportion of terrestrial OM was high in four periods: the last deglaciation (similar to 17.2 to similar to 12.2 ka), the early Holocene (similar to 10.6 to similar to 8.6 ka), the middle Holocene Thermal Optimum (similar to 7.7 to similar to 5 ka) and the late Holocene (similar to 4.2 to similar to 2 ka), whereas it was low in the intervening time periods. High TOC/TN values coincide with peak values of summer insolation, and thus the strongest EA summer monsoon during the early and middle Holocene: small drops in these ratios correspond to increasing and decreasing solar radiation in the deglacial period and the late Holocene, respectively. The four intervals with low TOC/TN ratios, as well as episodic drops of the ratios during the deglaciation and the early and late Holocene are concordant with the late last glacial (similar to 21 to similar to 17.2 ka), the Oldest (similar to 14.8 ka), the Older (similar to 13.3 ka) and the Younger Dryas (similar to 13 to similar to 11.5 ka), the 8.2 cold event (similar to 8.6-7.7 ka) and a late Holocene cold event (similar to 5-4.2 ka), and suggest a weakened EA summer monsoon during these times. Moreover, high frequency hydrological variability occurred during the early Holocene, heavy rainfall persisted during the middle Holocene, and precipitation intensity generally diminished after similar to 5 ka. The Tung-Yuan Pond sediment record indicates that the TOC/TN ratio can be used as a paleorainfall intensity proxy to trace variations in the EA summer monsoon strength in other small lakes. Crown Copyright
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| 13. |
- Zhao, Li Na, et al.
(författare)
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S100A9 induces aggregation-prone conformation in Abeta peptides : a combined experimental and simulation study
- 2013
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Ingår i: RSC Advances. - : RSC Publishing. - 2046-2069. ; 3:46, s. 24081-24089
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Tidskriftsartikel (refereegranskat)abstract
- Inflammation is one of the prominent pathological features in Alzheimer's disease (AD). Recently, there have been various proposed roles of neuroinflammation, such as the driving forces, bystander, byproduct or the neuroprotective response. Notwithstanding these diverse possible mechanisms, experiments have found that S100A9 is one of the pro-inflammatory proteins abundant and over-expressed in the inflammation sites of AD. In this paper, we examine the role of S100A9 in the oligomerization process of A beta peptides by means of replica exchange molecular dynamics simulation and experimental investigations. Our experiments, based on atomic force microscopy and Thioflavin T spectroscopic assays, have clearly indicated that the close interaction between S100A9 and A beta has significantly enhanced the A beta oligomerization. In line with the experimental observation, our simulation studies have revealed that the pro-inflammatory S100A9 protein interacts with the A beta peptides directly, mainly through hydrophobic interactions with the A beta central hydrophobic core region. In addition, the formation of hydrogen bonds between the residues of the S100A9 homodimer and the two ends of the A beta peptides is found to cause a straightening of the A beta(12-24) peptides. A more straight A beta(12-24) peptide with a higher beta-content then may function as a template to induce the folding of new incoming A beta peptides, which leads to the formation of aggregation-prone oligomers.
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