| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Zhou, Xian-Jing, et al.
(author)
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Thermo-sensitive Microgels Supported Gold Nanoparticles as Temperature-mediated Catalyst
- 2019
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In: Chinese Journal of Polymer Science. - : Springer Science and Business Media LLC. - 0256-7679 .- 1439-6203. ; 37:3, s. 235-242
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Journal article (peer-reviewed)abstract
- Microgels with a thermo-sensitive poly(N-isopropylacrylamide) (polyNIPAm) backbone and bis-imidazolium (VIM) ionic cross-links, denoted as poly(NIPAm-co-VIM), were successfully prepared. The as-synthesized ionic microgels were converted to nanoreactors, denoted as Au@PNI MGs, upon generation and immobilization of gold nanoparticles (Au NPs) of 5-8 nm in size into poly(NIPAm-co-VIM). The content of Au NPs in microgels could be regulated by controlling the 1,6-dibromohexane/vinylimidazole molar ratio in the quaternization reaction. The microgel-based nanoreactors were morphologically spherical and uniform in size, and presented reversible thermo-sensitive behavior with volume phase transition temperatures (VPTTs) at 39-40 degrees C. The Au@PNI MGs were used for the reduction of 4-nitrophenol, of which the catalytic activity could be modulated by temperature.
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| 3. |
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- 2019
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Journal article (peer-reviewed)
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| 4. |
- Cai, Jing, et al.
(author)
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Elucidating the mechanisms of atmospheric new particle formation in the highly polluted Po Valley, Italy
- 2024
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In: Atmospheric Chemistry and Physics. - 1680-7316 .- 1680-7324. ; 24:4, s. 2423-2441
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Journal article (peer-reviewed)abstract
- New particle formation (NPF) is a major source of aerosol particles and cloud condensation nuclei in the troposphere, playing an important role in both air quality and climate. Frequent NPF events have been observed in heavily polluted urban environments, contributing to the aerosol number concentration by a significant amount. The Po Valley region in northern Italy has been characterized as a hotspot for high aerosol loadings and frequent NPF events in southern Europe. However, the mechanisms of NPF and growth in this region are not completely understood. In this study, we conducted a continuous 2-month measurement campaign with state-of-the-art instruments to elucidate the NPF and growth mechanisms in northern Italy. Our results demonstrate that frequent NPF events (66% of all days during the measurement campaign) are primarily driven by abundant sulfuric acid (8.5×106cm-3) and basic molecules in this area. In contrast, oxygenated organic molecules from the atmospheric oxidation of volatile organic compounds (VOCs) appear to play a minor role in the initial cluster formation but contribute significantly to the consecutive growth process. Regarding alkaline molecules, amines are insufficient to stabilize all sulfuric acid clusters in the Po Valley. Ion cluster measurements and kinetic models suggest that ammonia (10ppb) must therefore also play a role in the nucleation process. Generally, the high formation rates of sub-2nm particles (87cm-3s-1) and nucleation-mode growth rates (5.1nmh-1) as well as the relatively low condensational sink (8.9×10-3s-1) will result in a high survival probability for newly formed particles, making NPF crucial for the springtime aerosol number budget. Our results also indicate that reducing key pollutants, such as SO2, amine and NH3, could help to substantially decrease the particle number concentrations in the Po Valley region.
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| 5. |
- Cheng, Shi-Ping, et al.
(author)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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In: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Journal article (peer-reviewed)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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| 6. |
- Jia, Kai-Hua, et al.
(author)
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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- 2021
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In: Horticulture Research. - : Oxford University Press (OUP). - 2052-7276 .- 2662-6810. ; 8:1
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Journal article (peer-reviewed)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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| 7. |
- Liang, Qi, et al.
(author)
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First-Principles Exploration of Hazardous Gas Molecule Adsorption on Pure and Modified Al60N60 Nanoclusters
- 2020
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In: Nanomaterials. - : MDPI. - 2079-4991. ; 10:11
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Journal article (peer-reviewed)abstract
- In this work, we use the first-principles method to study in details the characteristics of the adsorption of hazardous NO2, NO, CO2, CO and SO2 gas molecules by pure and heteroatom (Ti, Si, Mn) modified Al60N60 nanoclusters. It is found that the pure Al60N60 cluster is not sensitive to CO. When NO2, NO, CO2, CO and SO2 are adsorbed on Al60N60 cluster'stop.b, edge.a(p), edge.a(h), edge.a(p) andedge.a(h) sites respectively, the obtained configuration is the most stable for each gas. Ti, Si and Mn atoms prefer to stay on the top sites of Al60N60 cluster when these heteroatoms are used to modify the pure clusters. The adsorption characteristics of above hazardous gas molecules on these hetero-atom modified nanoclusters are also revealed. It is found that when Ti-Al60N60 cluster adsorbs CO and SO2, the energy gap decreases sharply and the change rate of gap is 62% and 50%, respectively. The Ti-modified Al60N60 improves the adsorption sensitivity of the cluster to CO and SO2. This theoretical work is proposed to predict and understand the basic adsorption characteristics of AlN-based nanoclusters for hazardous gases, which will help and guide researchers to design better nanomaterials for gas adsorption or detection.
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| 8. |
- Nie, Shuai, et al.
(author)
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Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
- 2023
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In: Horticulture Research. - : Oxford University Press. - 2662-6810 .- 2052-7276. ; 10:1
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Journal article (peer-reviewed)abstract
- The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
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| 9. |
- Owen, Christopher G, et al.
(author)
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Does initial breastfeeding lead to lower blood cholesterol in adult life? A quantitative review of the evidence.
- 2008
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In: American Journal of Clinical Nutrition. - 0002-9165 .- 1938-3207. ; 88:2, s. 305-14
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Journal article (peer-reviewed)abstract
- BACKGROUND: Earlier studies have suggested that infant feeding may program long-term changes in cholesterol metabolism. OBJECTIVE: We aimed to examine whether breastfeeding is associated with lower blood cholesterol concentrations in adulthood. DESIGN: The study consisted of a systematic review of published observational studies relating initial infant feeding status to blood cholesterol concentrations in adulthood (ie, aged >16 y). Data were available from 17 studies (17 498 subjects; 12 890 breastfed, 4608 formula-fed). Mean differences in total cholesterol concentrations (breastfed minus formula-fed) were pooled by using fixed-effect models. Effects of adjustment (for age at outcome, socioeconomic position, body mass index, and smoking status) and exclusion (of nonexclusive breast feeders) were examined. RESULTS: Mean total blood cholesterol was lower (P = 0.037) among those ever breastfed than among those fed formula milk (mean difference: -0.04 mmol/L; 95% CI: -0.08, 0.00 mmol/L). The difference in cholesterol between infant feeding groups was larger (P = 0.005) and more consistent in 7 studies that analyzed "exclusive" feeding patterns (-0.15 mmol/L; -0.23, -0.06 mmol/L) than in 10 studies that analyzed nonexclusive feeding patterns (-0.01 mmol/L; -0.06, 0.03 mmol/L). Adjustment for potential confounders including socioeconomic position, body mass index, and smoking status in adult life had minimal effect on these estimates. CONCLUSIONS: Initial breastfeeding (particularly when exclusive) may be associated with lower blood cholesterol concentrations in later life. Moves to reduce the cholesterol content of formula feeds below those of breast milk should be treated with caution.
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| 10. |
- Raposeiras-Roubin, Sergio, et al.
(author)
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Development and external validation of a post-discharge bleeding risk score in patients with acute coronary syndrome : The BleeMACS score
- 2018
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In: International Journal of Cardiology. - : ELSEVIER IRELAND LTD. - 0167-5273 .- 1874-1754. ; 254, s. 10-15
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Journal article (peer-reviewed)abstract
- Background: Accurate 1-year bleeding risk estimation after hospital discharge for acute coronary syndrome(ACS) may help clinicians guide the type and duration of antithrombotic therapy. Currently there are no predictive models for this purpose. The aim of this study was to derive and validate a simple clinical tool for bedside risk estimation of 1-year post-discharge serious bleeding in ACS patients.Methods: The risk score was derived and internally validated in the BleeMACS (Bleeding complications in a Multicenter registry of patients discharged with diagnosis of Acute Coronary Syndrome) registry, an observational international registry involving 15,401 patients surviving admission for ACS and undergoing percutaneous coronary intervention (PCI) from 2003 to 2014, engaging 15 hospitals from 10 countries located in America, Europe and Asia. External validation was conducted in the SWEDEHEART population, with 96,239 ACS patients underwent PCI and 93,150 without PCI.Results: Seven independent predictors of bleeding were identified and included in the BleeMACS score: age, hypertension, vascular disease, history of bleeding, malignancy, creatinine and hemoglobin. The BleeMACS risk score exhibited a C-statistic value of 0.71 (95% CI 0.68-0.74) in the derivation cohort and 0.72 (95% CI 0.67-0.76) in the internal validation sample. In the SWEDEHEART external validation cohort, the C-statistic was 0.65 (95% CI 0.64-0.66) for PCI patients and 0.63 (95% CI 0.62-0.64) for non-PCI patients. The calibration was excellent in the derivation and validation cohorts.Conclusions: The BleeMACS bleeding risk score is a simple tool useful for identifying those ACS patients at higher risk of serious 1-year post-discharge bleeding.
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