| 1. |
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- 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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| 4. |
- Kristan, Matej, et al.
(författare)
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The Sixth Visual Object Tracking VOT2018 Challenge Results
- 2019
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Ingår i: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).
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| 5. |
- Lu, Yingchang, et al.
(författare)
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Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians
- 2020
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association for Cancer Research. - 1055-9965 .- 1538-7755. ; 29:2, s. 477-486
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Tidskriftsartikel (refereegranskat)abstract
- Background: Risk variants identified so far for colorectal cancer explain only a small proportion of milial risk of this cancer, particularly in Asians.Methods: We performed a genome-wide association study (GWAS) of colorectal cancer in East Asians, cluding 23,572 colorectal cancer cases and 48,700 controls. To identify novel risk loci, we selected 60 omising risk variants for replication using data from 58,131 colorectal cancer cases and 67,347 controls European descent. To identify additional risk variants in known colorectal cancer loci, we performed nditional analyses in East Asians.Results: An indel variant, rs67052019 at 1p13.3, was found to be associated with colorectal cancer risk P = 3.9 x 10(-8) in Asians (OR per allele deletion = 1.13, 95% confidence interval = 1.08-1.18). This sociation was replicated in European descendants using a variant (rs2938616) in complete linkage sequilibrium with rs67052019 (P = 7.7 x 10(-3)). Of the remaining 59 variants, 12 showed an association P < 0.05 in the European-ancestry study, including rs11108175 and rs9634162 at P < 5 x 10(-8) and o variants with an association near the genome-wide significance level (rs60911071, P = 5.8 x 10(-8); 62558833, P = 7.5 x 10(-8)) in the combined analyses of Asian- and European-ancestry data. In addition, ing data from East Asians, we identified 13 new risk variants at 11 loci reported from previous GWAS.Conclusions: In this large GWAS, we identified three novel risk loci and two highly suggestive loci for lorectal cancer risk and provided evidence for potential roles of multiple genes and pathways in the iology of colorectal cancer. In addition, we showed that additional risk variants exist in many colorectal ncer risk loci identified previously.Impact: Our study provides novel data to improve the understanding of the genetic basis for colorectal ncer risk.
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| 6. |
- Pecunia, Vincenzo, et al.
(författare)
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Roadmap on energy harvesting materials
- 2023
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Ingår i: Journal of Physics. - : IOP Publishing. - 2515-7639. ; 6:4
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Tidskriftsartikel (refereegranskat)abstract
- Ambient energy harvesting has great potential to contribute to sustainable development and address growing environmental challenges. Converting waste energy from energy-intensive processes and systems (e.g. combustion engines and furnaces) is crucial to reducing their environmental impact and achieving net-zero emissions. Compact energy harvesters will also be key to powering the exponentially growing smart devices ecosystem that is part of the Internet of Things, thus enabling futuristic applications that can improve our quality of life (e.g. smart homes, smart cities, smart manufacturing, and smart healthcare). To achieve these goals, innovative materials are needed to efficiently convert ambient energy into electricity through various physical mechanisms, such as the photovoltaic effect, thermoelectricity, piezoelectricity, triboelectricity, and radiofrequency wireless power transfer. By bringing together the perspectives of experts in various types of energy harvesting materials, this Roadmap provides extensive insights into recent advances and present challenges in the field. Additionally, the Roadmap analyses the key performance metrics of these technologies in relation to their ultimate energy conversion limits. Building on these insights, the Roadmap outlines promising directions for future research to fully harness the potential of energy harvesting materials for green energy anytime, anywhere.
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| 7. |
- Wan, Cheng-Liang, et al.
(författare)
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Dynamics of slow electrons transmitting through straight glass capillary and tapered glass capillary
- 2016
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Ingår i: Wuli xuebao. - : Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences. - 1000-3290. ; 65:20
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Tidskriftsartikel (refereegranskat)abstract
- It has been found that the transmission rate of the electrons through insulating capillaries as a function of time/incident charge is not the same as that of the ions. The question arises that by using the electrons, if the negative charge patches can be formed to facilitate the transmission of the following electrons, thereby substantiating that the so-called guiding effect works also for electrons. This study aims to observe the time evolutions of the transmission of electrons through a straight glass tube and a tapered glass capillary. This will reveal the details of how and (or) if the negative charge patches can be formed when the electrons transport through them. In this work, a set of MCP/phosphor two-dimensional detection system based on Labview platform is developed to obtain the time evolution of the angular distribution of the transmitted electrons. The pulsed electron beams are obtained to test our detection system. The time evolution of the angular profile of 1.5 keV electrons transmitting through the glass tube/capillary is observed. The transmitted electrons are observed on the detector for a very short time and disappear for a time and then appear again for both the glass tube and tapered glass capillary, leading to an oscillation. The positive charge patches are formed in the insulating glass tube and tapered glass capillary since the secondary electron emission coefficient for the incident energy is larger than 1. It is due to the fact that fast discharge of the deposited charge leads to the increase of the transmission rate, while the fast blocking of the incident electrons due to the deposited positive charge leads to the decrease of the transmission rate. The geometrical configuration of the taper glass capillary tends to make the secondary electrons deposited at the exit part to form the negative patches that facilitate the transmission of electrons. This suggests that if the stable transmission needs to be reached for producing the electron micro-beam by using tapered glass capillaries, the steps must be taken to have the proper grounding and shielding of the glass capillaries and tubes. Our results show a difference in transmission through the insulating capillary between electrons and highly charged ions.
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| 8. |
- Bai, Yang, et al.
(författare)
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Geometry design of tethered small-molecule acceptor enables highly stable and efficient polymer solar cells
- 2023
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Ingår i: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- With the power conversion efficiency of binary polymer solar cells dramatically improved, the thermal stability of the small-molecule acceptors raised the main concerns on the device operating stability. Here, to address this issue, thiophene-dicarboxylate spacer tethered small-molecule acceptors are designed, and their molecular geometries are further regulated via the thiophene-core isomerism engineering, affording dimeric TDY-alpha with a 2, 5-substitution and TDY-beta with 3, 4-substitution on the core. It shows that TDY-alpha processes a higher glass transition temperature, better crystallinity relative to its individual small-molecule acceptor segment and isomeric counterpart of TDY-beta, and amore stablemorphology with the polymer donor. As a result, the TDY-alpha based device delivers a higher device efficiency of 18.1%, and most important, achieves an extrapolated lifetime of about 35000 hours that retaining 80% of their initial efficiency. Our result suggests that with proper geometry design, the tethered small-molecule acceptors can achieve both high device efficiency and operating stability.
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| 9. |
- Liu, Chun-Yan, et al.
(författare)
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Massively Parallel Aligned Poly(vinylidene fluoride) Nanofibrils in All-Organic Dielectric Polymer Composite Films for Electric Energy Storage
- 2023
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 56:4, s. 1481-1491
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Tidskriftsartikel (refereegranskat)abstract
- It is a formidable challenge to combine the perform-ance advantages of linear and nonlinear polymer dielectrics for developing all-organic film capacitors with high energy density and low loss. In this work, massively parallel aligned poly(vinylidene fluoride) (PVDF) nanofibrils were in situ fabricated for the first time in the polyethylene (PE) matrix via a multistage stretching technology involving hot stretching and solid-state stretching at an elevated temperature. The largely enhanced interfacial area of PVDF nanofibrils could effectively induce interfacial polarization, imparting PE composite films with a high dielectric constant of 4.50. More interestingly, the nanoconfinement effect of PVDF nanofibrils greatly restricted the migration of free electrons and impurity ions, and an impressive breakdown strength of 624 MV m-1 was obtained. As a result, the as-prepared PE/PVDF composite films exhibited an attractive discharged energy density of as high as 6.4 J cm-3, which was more than 10 times of the conventional counterparts, and outperformed the current linear dielectric polymers. The ingenious structure design of in situ nonlinear dielectric nanofibrils provides a promising approach to maximize the advantageous polarizations and minimize the disadvantageous polarizations in the linear and nonlinear polymer dielectric blends, achieving all-organic polymer dielectric composite films with high energy density and low loss.
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| 10. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 11. |
- Li, Zhi-Hua, et al.
(författare)
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Biochemical and physiological responses in liver and muscle of rainbow trout after long-term exposure to propiconazole
- 2010
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Ingår i: Ecotoxicology and Environmental Safety. - : Elsevier Inc. - 0147-6513 .- 1090-2414. ; 73:6, s. 1391-1396
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Tidskriftsartikel (refereegranskat)abstract
- In this study, the chronic toxic effects of PCZ, a triazole fungicide commonly present in surface and ground water, on morphological indices, ROS generation and RNA/DNA ratio in liver and white muscle of rainbow trout were investigated. Fish were exposed at sublethal concentrations of PCZ (0.2, 50 and 500mugL(-1)) for 7, 20 and 30d. Compared with the control, there were significant lower CF and HSI in fish exposed at the highest concentration of PCZ. ROS levels in both tissues increased significantly at higher PCZ concentrations (50 and 500mugL(-1)) after 20d and above, as well as in muscle of fish exposed at lowest PCZ concentration (0.2mugL(-1)) after 30d. The hepatic antioxidant enzymes (SOD and CAT) activities were induced significantly at higher concentrations (50, 500mugL(-1)) of PCZ after 20d and at 50mugL(-1) after 30d. Additional, hepatic SOD activity was significantly induced at 0.2mugL(-1) after 30d. Compared with the hepatic antioxidant enzymes activities in fish exposed to 50mugL(-1) of PCZ, there was a decreasing trend in those exposed to 500mugL(-1) after 30d exposure. However, both the antioxidant enzymes activities were significantly inhibited in muscle of fish exposed to 500mugL(-1) PCZ after 30d. Moreover there was significant lower RNA/DNA ratio in both tissues after long-term exposure to higher concentration of PCZ. In short, environmental concentrations of PCZ could not induce obvious impacts on fish, but long-term exposure to higher concentrations of CBZ could affect seriously the health status of fish.
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| 12. |
- Li, Zhi-Hua, et al.
(författare)
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Effects of exposure to sublethal propiconazole on intestine-related biochemical responses in rainbow trout, Oncorhynchus mykiss
- 2010
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Ingår i: Chemico-Biological Interactions. - : Elsevier BV. - 0009-2797 .- 1872-7786. ; 185:3, s. 241-246
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Tidskriftsartikel (refereegranskat)abstract
- The effect of long-term (30 days) exposure to PCZ (0.2, 50, and 500 microg l(-1)) on intestine-related biochemical markers in rainbow trout was investigated. Multiple biomarkers were measured, including digestive enzymes (proteolytic enzymes and amylase), antioxidant responses (TBARS, CP, SOD, CAT, GR and GPx) and energy metabolic parameters (RNA/DNA ratio, Na(+)-K(+)-ATPase). Exposure to 500 microg l(-1) PCZ led to significantly inhibited (p<0.01) proteolytic enzyme and amylase activity. Activities of the antioxidant enzymes SOD, CAT, and GPx gradually increased at lower PCZ concentrations (0.2 and 50 microg l(-1)). At the highest concentration (500 microg l(-1)), oxidative stress was apparent as significant higher (p<0.05) lipid peroxidation and protein carbonyls, associated with an inhibition of antioxidant enzymes activity. Moreover, energy metabolic parameters (RNA/DNA ratio, Na(+)-K(+)-ATPase) were significantly inhibited (p<0.01) in the intestines of fish exposed to 500 microg l(-1) PCZ, compared with controls. We suggest that long-term exposure to PCZ could result in several responses in intestine-related biochemical markers, which potentially could be used as indicators for monitoring residual PCZ present in the aquatic environment.
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| 13. |
- Li, Zhi-Hua, et al.
(författare)
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Effects of exposure to sublethal propiconazole on the antioxidant defense system and Na+-K+-ATPase activity in brain of rainbow trout, Oncorhynchus mykiss
- 2010
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Ingår i: Aquatic Toxicology. - : Elsevier. - 0166-445X .- 1879-1514. ; 98:3, s. 297-303
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Tidskriftsartikel (refereegranskat)abstract
- Propiconazole (PCZ), a triazole fungicide, is widely present in the aquatic environment, but little is known regarding its chronic toxicity in the fish brain. This study assessed the effects of long-term exposure to PCZ on the antioxidant defense system and Na(+)-K(+)-ATPase activity of rainbow trout brain. Fish were exposed to sublethal concentrations of PCZ (0.2, 50, and 500 microg/l) for 7, 20, and 30 days, respectively. Oxidative stress indices (reactive oxygen species, lipid peroxidation, and carbonyl protein) and antioxidant parameters (superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase, and reduced glutathione) were measured, as well as Na(+)-K(+)-ATPase activity. Adaptive responses to PCZ-induced stress were observed at 7 days. With prolonged exposure, significantly higher levels of oxidative indices were indicative of oxidative stress, as also were the significant inhibition of antioxidant enzyme activity and reduced glutathione content. Na(+)-K(+)-ATPase activity was significantly inhibited after prolonged exposure. Chemometrics of all parameters by principal component analysis, enabled the separation of sampled individuals into four groups with 93.39% of total accumulated variance. A low level of oxidative stress can induce the adaptive responses of the antioxidant defense system, while prolonged exposure to PCZ may lead to serious oxidative damage in fish brain. We suggest that selected biochemical markers in fish brain could be used as potential biomarkers for monitoring residual fungicides present in the aquatic environments.
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| 14. |
- Li, Zhi-Hua, et al.
(författare)
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Modulation of glutathione-related antioxidant defense system of fish chronically treated by the fungicide propiconazole
- 2010
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Ingår i: Comparative Biochemistry and Physiology - Part C. - : Elsevier. - 1532-0456 .- 1878-1659. ; 152:3, s. 392-398
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Tidskriftsartikel (refereegranskat)abstract
- Recently, residual fungicides are generally recognized as relevant sources of aquatic environmental pollutants. However, the toxicological effects of these contaminants have not been adequately researched. In this study, the chronic effect of PCZ, a triazole-containing fungicide commonly present in aquatic environment, on GSH-related antioxidant system and oxidative stress indices of rainbow trout (Oncorhynchus mykiss) were investigated. Fish were exposed at sub-lethal concentrations of PCZ (0.2, 50 and 500 microg/L) for 7, 20 and 30 days. GSH levels and GSH-related enzyme activities, including GPx, GR and GST, were quantified in three tissues-liver, gill and muscle. The levels of LPO and CP were also measured as makers of oxidative damage. In addition, the correlations of the measured parameters in various tissues were evaluated by using PCA. The results of this study indicate that chronic exposure of PCZ has resulted in different responses in various tissues and the gill was the most sensitive tissue; however, before these parameters are used as potential biomarkers for monitoring residual fungicides in aquatic environment, more detailed experiments in laboratory need to be performed in the future.
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| 15. |
- Shi, Tian-Le, et al.
(författare)
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High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
- 2024
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Ingår i: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 195:1, s. 652-670
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Tidskriftsartikel (refereegranskat)abstract
- Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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| 16. |
- Chen, Mei-Qin, et al.
(författare)
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Arabidopsis NMD3 is required for nuclear export of 60S ribosomal subunits and affects secondary cell wall thickening
- 2012
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:4, s. 35904-35904
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Tidskriftsartikel (refereegranskat)abstract
- NMD3 is required for nuclear export of the 60S ribosomal subunit in yeast and vertebrate cells, but no corresponding function of NMD3 has been reported in plants. Here we report that Arabidopsis thaliana NMD3 (AtNMD3) showed a similar function in the nuclear export of the 60S ribosomal subunit. Interference with AtNMD3 function by overexpressing a truncated dominant negative form of the protein lacking the nuclear export signal sequence caused retainment of the 60S ribosomal subunits in the nuclei. More interestingly, the transgenic Arabidopsis with dominant negative interference of AtNMD3 function showed a striking failure of secondary cell wall thickening, consistent with the altered expression of related genes and composition of cell wall components. Observation of a significant decrease of rough endoplasmic reticulum (RER) in the differentiating interfascicular fiber cells of the transgenic plant stems suggested a link between the defective nuclear export of 60S ribosomal subunits and the abnormal formation of the secondary cell wall. These findings not only clarified the evolutionary conservation of NMD3 functions in the nuclear export of 60S ribosomal subunits in yeast, animals and plants, but also revealed a new facet of the regulatory mechanism underlying secondary cell wall thickening in Arabidopsis. This new facet is that the nuclear export of 60S ribosomal subunits and the formation of RER may play regulatory roles in coordinating protein synthesis in cytoplasm and transcription in nuclei.
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| 17. |
- Chen, Shi-Peng, et al.
(författare)
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Guanidine-based protic ionic liquids as highly efficient intermolecular scissors for dissolving natural cellulose
- 2023
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Ingår i: Green Chemistry. - : Royal Society of Chemistry. - 1463-9262 .- 1463-9270. ; 25:22, s. 9322-9334
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Tidskriftsartikel (refereegranskat)abstract
- The development of highly efficient and environmentally friendly solvents for dissolving cellulose, which is the most abundant natural polymer on Earth, remains a challenge, hindering its full utilization. Herein, a green protic ionic liquid, 1,1,3,3-tetramethylguanidinium methoxyacetate ([TMGH][MAA]), was found to exhibit attractive capacity to dissolve natural cellulose with an appropriate TMG/MAA molar ratio of 7 : 3 at 80 degrees C. The solubility of cotton linter and ultra-high molecular weight cotton fibers reached 13% (w/w) and 3% (w/w), respectively, surpassing that of most solvent systems currently used for the dissolution of cellulose. The experimental and simulation results verified that the excellent dissolution ability of [TMGH][MAA] for cellulose is mainly attributed to the destruction of the intrinsic hydrogen-bond networks in cellulose by the synergistic interactions of the [TMGH] cations and [MAA] anions with the hydroxyl groups in the cellulose chains, acting as highly efficient "intermolecular scissors". The superiority of this novel dissolution system was further demonstrated by the remarkable comprehensive properties of the regenerated cellulose film including satisfactory thermostability, high transparency, and excellent mechanical properties. Furthermore, the satisfactory recovery performance of this solvent highlights its significant feasibility for large-scale industrial manufacturing. The proposed [TMGH][MAA] in this study exhibits great potential as a next-generation processing solvent for dissolving, and thus processing cellulose, promoting the sustainable development of high-value-added cellulose materials.
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| 18. |
- Hua, Dong, et al.
(författare)
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Small interfering RNA-directed targeting of toll-like receptor 4 inhibits human prostate cancer cell invasion, survival, and tumorigenicity
- 2009
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Ingår i: Molecular Immunology. - : Elsevier BV. - 0161-5890 .- 1872-9142. ; 46:15, s. 2876-2884
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Tidskriftsartikel (refereegranskat)abstract
- A major cause of tumor treatment failure is cancer cell metastasis. Toll-like receptor 4 (TLR4)-mediated signaling has been implicated in tumor cell invasion, survival, and metastasis in a variety of cancers. In this study, we investigated the biological roles of TLR4 in prostate metastatic cell invasion and survival, and the potential of gene silencing of TLR4 using small interfering RNA (siRNA) for treatment of cancer. In cultured human prostate cancer cell lines, TLR4 were higher PC3 and DU145 as compared with the poorly metastatic LNCaP indicating that up-regulation of TLR4 was positively correlated with metastasis of tumor cell. In the highly metastatic cancer cell PC3, gene silencing of TLR4 using siRNA significantly inhibited TLR4 mRNA expression and protein level. Knockdown of TLR4 in PC3 cells resulted in a dramatic reduction of tumor cell migration and invasion as indicated by a Matrigel invasion assay. Furthermore, TLR4 siRNA suppressed cell viability and ultimately caused the induction of apoptotic cell death. The effects were associated with abrogating TLR4-mediated signaling to downstream target molecules such as myeloid differentiation factor 88 (MyD88), adaptor-inducing IFN-beta (TRIF), and interferon regulatory factor-1 (IRF-1). In a mouse prostate cancer model, administration with the plasmid construct expressing siRNA for TLR4 obviously inhibited established tumor growth and survival. These studies revealed evidence of a multifaceted signaling network operating downstream of TLR4-mediated tumor cell invasion, proliferation, and survival. Thus, RNA interference-directed targeting of TLR4 may raise the potential of its application for cancer therapy.
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| 19. |
- Jia, Kai-Hua, et al.
(författare)
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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- 2021
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Ingår i: Horticulture Research. - : Oxford University Press (OUP). - 2052-7276 .- 2662-6810. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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| 20. |
- Jiang, Bin, et al.
(författare)
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Experimental observation of non-Abelian topological acoustic semimetals and their phase transitions
- 2021
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Ingår i: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 17, s. 1239-1246
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Tidskriftsartikel (refereegranskat)abstract
- Topological phases of matter connect mathematical principles to real materials, and may shape future electronic and quantum technologies. So far, this discipline has mostly focused on single-gap topology described by topological invariants such as Chern numbers. Here, based on a tunable kagome model, we observe non-Abelian band topology and its transitions in acoustic semimetals, in which the multi-gap Hilbert space plays a key role. In non-Abelian semimetals, the topological charges of band nodes are converted through the braiding of nodes in adjacent gaps, and their behaviour cannot be captured by conventional topological band theory. Using kagome acoustic metamaterials and pump–probe measurements, we demonstrate the emergence of non-Abelian topological nodes, identify their dispersions and observe the induced multi-gap topological edge states. By controlling the geometry of the metamaterials, topological transitions are induced by the creation, annihilation, merging and splitting of band nodes. This reveals the underlying rules for the conversion and transfer of non-Abelian topological charges in multiple bandgaps. The resulting laws that govern the evolution of band nodes in non-Abelian multi-gap systems should inspire studies on multi-band topological semimetals and multi-gap topological out-of-equilibrium systems.
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| 21. |
- Li, Zhi-Hua, et al.
(författare)
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Enzymatic alterations and RNA/DNA ratio in intestine of rainbow trout, Oncorhynchus mykiss, induced by chronic exposure to carbamazepine
- 2010
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Ingår i: Ecotoxicology. - : Springer Science and Business Media LLC. - 0963-9292 .- 1573-3017. ; 19:5, s. 872-8
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the effect of long-term exposure to carbamazepine (CBZ) on the enzymatic alterations and RNA/DNA ratio in intestine tissue of rainbow trout. Fish were exposed to sublethal concentrations of CBZ (1.0 microg/l, 0.2 or 2.0 mg/l) for 42 days. Digestive enzymes (proteolytic enzymes and amylase) and energy metabolic enzyme (Na(+)-K(+)-ATPase) and antioxidant enzymes (superoxide dismutase [SOD], catalase [CAT], glutathione peroxidase [GPx], and glutathione reductase [GR]) in fish intestine were measured. In addition, intestinal RNA/DNA ratio was determined after 42 days exposure. Carbamazepine exposure at 2.0 mg/l led to significantly inhibited (P < 0.05) activity of Na(+)-K(+)-ATPase. Activities of the antioxidant enzymes SOD, CAT, and GPx in CBZ-treated groups gradually increased at lower concentration of CBZ (1.0 microg/l and 0.2 mg/l), then significantly inhibited (P < 0.05) at 2.0 mg/l. After 42 days, the RNA/DNA ratio in fish intestine was significantly lower (P < 0.05) in groups exposed to CBZ at 2.0 mg/l than in other groups. However, there was no statistical significance (P > 0.05) in the activities of digestive enzymes (proteolytic enzyme and amylase) and GR in all groups. In short, prolonged exposure to CBZ resulted in different responses of various enzymes and significantly lower RNA/DNA ratio in fish intestine. Furthermore, molecular and genetic mechanisms of these physiological responses in fish are not clear, which need to be further studied.
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| 22. |
- Li, Zhi-Hua, et al.
(författare)
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Hepatic antioxidant status and hematological parameters in rainbow trout, Oncorhynchus mykiss, after chronic exposure to carbamazepine
- 2010
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Ingår i: Chemico-Biological Interactions. - : Elsevier BV. - 0009-2797 .- 1872-7786. ; 183:1, s. 98-104
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Tidskriftsartikel (refereegranskat)abstract
- Recently, residual pharmaceuticals are generally recognized as relevant sources of aquatic environmental pollutants. However, the toxicological effects of these contaminants have not been adequately researched. In this study, the chronic toxic effect of carbamazepine (CBZ), an anticonvulsant drug commonly present in surface and ground water, on hepatic antioxidant status and hematological parameters of rainbow trout were investigated. Fish were exposed at sublethal concentrations of CBZ (1.0mug/l, 0.2mg/l and 2.0mg/l) for 7, 21 and 42 days. Compared to the control group, fish exposed at higher concentration (0.2mg/l or 2.0mg/l) of CBZ showed significantly higher levels of hemoglobin, ammonia and glucose, and significantly higher plasma enzymes activities. During the exposure duration, erythrocyte count, hematocrit, mean erythrocyte hemoglobin, mean erythrocyte volume, mean color concentration and total protein content in all groups were not significantly different. At the highest test concentration (2.0mg/l) of CBZ, oxidative stress was apparent as reflected by the significant higher lipid peroxidation and protein carbonyl levels in liver after 42 days exposure, associated with an inability to induce antioxidant enzymes activities including superoxide dismutase, glutathione peroxidase and glutathione reductase. After 42 days exposure, reduced glutathione level was significantly decreased in the fish exposed at 0.2mg/l CBZ, compared with the control. In short, CBZ-induced physiological and biochemical responses in fish were reflected in the oxidant stress indices and hematological parameters. These results suggest that hepatic antioxidant responses and hematological parameter could be used as potential biomarkers for monitoring residual pharmaceuticals present in aquatic environment.
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| 23. |
- Li, Zhi-Hua, et al.
(författare)
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Modulation of antioxidant defence system in brain of rainbow trout (Oncorhynchus mykiss) after chronic carbamazepine treatment
- 2010
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Ingår i: Comparative Biochemistry and Physiology - Part C. - : Elsevier BV. - 1532-0456 .- 1878-1659. ; 151:1, s. 137-41
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the effect of long-term exposure to CBZ on the antioxidant system in brain tissue of rainbow trout. Fish were exposed to sublethal concentrations of CBZ (1.0mug/L, 0.2mg/L or 2.0mg/L) for 7, 21, and 42days. Oxidative stress indices (LPO and CP) and activities of antioxidant enzymes (SOD, CAT, GPx and GR) in fish brain were measured. In addition, non-enzymatic antioxidant (GSH) was determined after 42days exposure. Carbamazepine exposure at 0.2mg/L led to significant increases (p<0.05) of LPO and CP after 42days and, at 2.0mg/L, after 21days. Activities of the antioxidant enzymes SOD, CAT, and GPx in CBZ-treated groups slightly increased during the first period (7days). However, activities of all measured antioxidant enzymes were significantly inhibited (p<0.05) at 0.2mg/L exposure after 42days and after 21days at 2.0mg/L. After 42days, the content of GSH in fish brain was significantly lower (p<0.05) in groups exposed to CBZ at 0.2mg/L and 2.0mg/L than in other groups. Prolonged exposure to CBZ resulted in excess reactive oxygen species formation, finally resulting in oxidative damage to lipids and proteins and inhibited antioxidant capacities in fish brain. In short, a low level of oxidative stress could induce the adaptive responses of antioxidant enzymes, but long-term exposure to CBZ could lead to serious oxidative damage in fish brain.
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| 24. |
- Li, Zhi-Hua, et al.
(författare)
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Physiological condition status and muscle-based biomarkers in rainbow trout (Oncorhynchus mykiss), after long-term exposure to carbamazepine
- 2010
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Ingår i: Journal of Applied Toxicology. - : Wiley. - 0260-437X .- 1099-1263. ; 30:3, s. 197-203
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Tidskriftsartikel (refereegranskat)abstract
- Recently, residual pharmaceuticals are generally recognized as relevant sources of aquatic environmental pollutants. However, the toxicological effects of these contaminants have not been adequately researched. In this study, the chronic toxic effects of carbamazepine (CBZ), an anticonvulsant pharmaceutical commonly present in surface and ground water, on physiological condition status and muscle-based biomarkers of rainbow trout were investigated. Fish were exposed at sublethal concentrations of CBZ (1.0 microg l(-1), 0.2 mg l(-1) and 2.0 mg l(-1)) for 42 days. Compared with the control, there was a significant lower (P < 0.05) condition factor in fish exposed at the highest concentration of CBZ (2.0 mg l(-1)), but the hepatosomatic indices in all groups were not significant changes. At lower CBZ concentration (1.0 microg l(-1), 0.2 mg l(-1)), the antioxidant enzyme activities were induced slightly, except catalase, while at the highest concentration (2.0 mg l(-1)) oxidative stress was apparent as reflected by the significant higher lipid peroxidation and protein carbonyls in the fish muscle, associated with a significant inhibition of antioxidant enzymes activities. Moreover, energy metabolic parameters (RNA-DNA ratio, Na(+)-K(+)-ATPase) were significantly inhibited in muscle of the fish exposed at the highest concentration (2.0 mg l(-1)), compared with the control. In short, CBZ-induced physiological and biochemical responses in fish were reflected in parameters measured in this study, which suggest that these biomarkers could be used as potential indicators for monitoring residual pharmaceuticals present in aquatic environment.
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| 25. |
- Li, Zhi-Hua, et al.
(författare)
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Responses of antioxidant status and Na+-K+-ATPase activity in gill of rainbow trout, Oncorhynchus mykiss, chronically treated with carbamazepine
- 2009
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Ingår i: Chemosphere. - : Elsevier. - 0045-6535 .- 1879-1298. ; 77:11, s. 1476-1481
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Tidskriftsartikel (refereegranskat)abstract
- In recent years, chemical pollution by the residual pharmaceuticals has been increasingly important issue due to its widely present in the aquatic environment. However, the toxicological effects of residual pharmaceuticals on fish have not been adequately researched. The aim of this work is to investigate the toxic effect of CBZ, an anticonvulsant drug commonly present in aquatic environment, on antioxidant status and Na+-K+-ATPase in gill of rainbow trout exposed to sublethal CBZ (1.0 microg L(-1), 0.2 mg L(-1) and 2.0 mg L(-1)) for 7, 21 and 42 d. After prolonged exposure of CBZ at higher test concentration (0.2 or 2.0 mg L(-1)), oxidative stress was apparent as reflected by the significant higher LPO and CP levels in fish gill, as well as the significant inhibition of antioxidant enzymes activities including SOD, CAT, GR and GPx. Besides, reduced glutathione level and Na+-K+-ATPase activity were significantly lower than those of the control after 42 d of exposure to CBZ at higher test concentration (0.2 or 2.0 mg L(-1)). The results of this study indicate that chronic exposure of CBZ has altered multiple physiological indices in fish gill; however, before those parameters are used as special biomarkers for monitoring residual pharmaceuticals in aquatic environment, more detailed experiments in laboratory need to be performed in the future.
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| 26. |
- Shi, Tian-Le, et al.
(författare)
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Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
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| 27. |
- Tian, Xue-Chan, et al.
(författare)
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Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification
- 2024
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Ingår i: Horticulture Research. - 2662-6810 .- 2052-7276. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.
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| 28. |
- Yan, Xue-Mei, et al.
(författare)
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Unraveling the evolutionary dynamics of the TPS gene family in land plants
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.
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| 29. |
- Yang, Zhi-Bo, et al.
(författare)
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Stable subspace dimension reduced MUSIC for blade tip timing
- 2023
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Ingår i: Journal of Sound and Vibration. - : Elsevier. - 0022-460X .- 1095-8568. ; 545
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Tidskriftsartikel (refereegranskat)abstract
- Multiple signal classification (MUSIC) is a parameter extraction method for blade tip timing to suppress the under-sampled problem. Its faster version, subspace dimension reduced MUSIC (SDR-MUSIC), has been proposed, which uses a single noise vector instead of the whole noise subspace to reduce computational complexity. However, the principle of random noise vector selection leads to instability in frequency identification. Therefore, we replace the random vector with the min-norm vector to obtain a stable SDR-MUSIC (SSDR-MUSIC). The superiority of the min-norm vector can be mathematically proven by the location of the zeros of the polynomial. Simulated and experimental tests indicate that SSDR-MUSIC gains stability when the min-norm vector is used while maintaining computational efficiency.
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