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| 2. |
- 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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| 3. |
- Ahola, Virpi, et al.
(author)
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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
- 2014
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4737-
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Journal article (peer-reviewed)abstract
- Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
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| 4. |
- Calabrese, Claudia, et al.
(author)
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Genomic basis for RNA alterations in cancer
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
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Journal article (peer-reviewed)abstract
- Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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| 5. |
- Jiang, Kui, et al.
(author)
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Suppressed recombination loss in organic photovoltaics adopting a planar-mixed heterojunction architecture
- 2022
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In: Nature Energy. - : NATURE PORTFOLIO. - 2058-7546. ; 7:11, s. 1076-1086
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Journal article (peer-reviewed)abstract
- At present, high-performance organic photovoltaics mostly adopt a bulk-heterojunction architecture, in which exciton dissociation is facilitated by charge-transfer states formed at numerous donor-acceptor (D-A) heterojunctions. However, the spin character of charge-transfer states originated from recombination of photocarriers allows relaxation to the lowest-energy triplet exciton (T-1) at these heterojunctions, causing photocurrent loss. Here we find that this loss pathway can be alleviated in sequentially processed planar-mixed heterojunction (PMHJ) devices, employing donor and acceptor with intrinsically weaker exciton binding strengths. The reduced D-A intermixing in PMHJ alleviates non-geminate recombination at D-A contacts, limiting the chance of relaxation, thus suppressing T-1 formation without sacrificing exciton dissociation efficiency. This resulted in devices with high power conversion efficiencies of >19%. We elucidate the working mechanisms for PMHJs and discuss the implications for material design, device engineering and photophysics, thus providing a comprehensive grounding for future organic photovoltaics to reach their full promise. Organic solar cells with a bulk-heterojunction architecture suffer from photocurrent loss driven by triplet states. Now, Jiang et al. show that sequentially deposited donor-acceptor planar-mixed heterojunctions suppress triplet formation, enabling efficiencies over 19%.
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| 6. |
- Liu, Junwei, et al.
(author)
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Polymer synergy for efficient hole transport in solar cells and photodetectors
- 2023
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In: Energy & Environmental Science. - : ROYAL SOC CHEMISTRY. - 1754-5692 .- 1754-5706.
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Journal article (peer-reviewed)abstract
- Hole transport materials (HTMs) have greatly advanced the progress of solution-based electronic devices in the past few years. Nevertheless, most devices employing dopant-free organic HTMs can only deliver inferior performance. In this work, we introduced a novel "polymer synergy" strategy to develop versatile dopant-free polymer HTMs for quantum dot/perovskite solar cells and photodetectors. With this synergy strategy, the optical, electrical and aggregation properties of polymer HTMs can be modulated, resulting in complementary absorption, high hole mobility, favorable energy landscape and moderate aggregation. Moreover, a clear orientational transition was observed for the developed HTMs with a 9-fold increase in the face-on/edge-on ratio, providing a highway-like carrier transport for electronic devices, as revealed by in situ characterization and ultrafast transient absorption. With these benefits, the photovoltaic and photodetection performance of quantum dot devices were boosted from 11.8% to 13.5% and from 2.95 x 10(12) to 3.41 x 10(13) Jones (over a 10-fold increase), respectively. Furthermore, the developed polymer HTMs can also significantly enhance the photovoltaic and photodetection performance of perovskite devices from 15.1% to 22.7% and from 2.7 x 10(12) to 2.17 x 10(13)Jones with the same device structure, indicating their great application potential in the emerging optoelectronics.
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| 7. |
- Tuohimaa, Pentti, et al.
(author)
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Gene Expression Profiles in Human and Mouse Primary Cells Provide New Insights into the Differential Actions of Vitamin D-3 Metabolites
- 2013
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:10
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Journal article (peer-reviewed)abstract
- 1 alpha,25-Dihydroxyvitamin D-3 (1 alpha,25(OH)(2)D-3) had earlier been regarded as the only active hormone. The newly identified actions of 25-hydroxyvitamin D-3 (25(OH)D-3) and 24R,25-dihydroxyvitamin D-3 (24R,25(OH)(2)D-3) broadened the vitamin D-3 endocrine system, however, the current data are fragmented and a systematic understanding is lacking. Here we performed the first systematic study of global gene expression to clarify their similarities and differences. Three metabolites at physiologically comparable levels were utilized to treat human and mouse fibroblasts prior to DNA microarray analyses. Human primary prostate stromal P29SN cells (hP29SN), which convert 25(OH)D-3 into 1 alpha,25(OH)(2)D-3 by 1 alpha-hydroxylase (encoded by the gene CYP27B1), displayed regulation of 164, 171, and 175 genes by treatment with 1 alpha,25(OH)(2)D-3, 25(OH)D-3, and 24R,25(OH)(2)D-3, respectively. Mouse primary Cyp27b1 knockout fibroblasts (mCyp27b1(-/-)), which lack 1 alpha-hydroxylation, displayed regulation of 619, 469, and 66 genes using the same respective treatments. The number of shared genes regulated by two metabolites is much lower in hP29SN than in mCyp27b1(-/-). By using DAVID Functional Annotation Bioinformatics Microarray Analysis tools and Ingenuity Pathways Analysis, we identified the agonistic regulation of calcium homeostasis and bone remodeling between 1 alpha,25(OH)(2)D-3 and 25(OH)D-3 and unique non-classical actions of each metabolite in physiological and pathological processes, including cell cycle, keratinocyte differentiation, amyotrophic lateral sclerosis signaling, gene transcription, immunomodulation, epigenetics, cell differentiation, and membrane protein expression. In conclusion, there are three distinct vitamin D-3 hormones with clearly different biological activities. This study presents a new conceptual insight into the vitamin D-3 endocrine system, which may guide the strategic use of vitamin D-3 in disease prevention and treatment.
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| 8. |
- Wang, Shuying, et al.
(author)
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Application of geopolymers for treatment of industrial solid waste containing heavy metals: State-of-the-art review
- 2023
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In: Journal of Cleaner Production. - : Elsevier BV. - 0959-6526. ; 390
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Research review (peer-reviewed)abstract
- Metallurgy, mineral processing, waste disposal, and other industries produce large amounts of industrial solid waste containing heavy metals (ISWCHM), which poses a serious threat to the ecological environment. Geopolymers are aluminosilicate inorganic polymers that have the advantages of high strength, good corrosion resistance, and low carbon emission during production. The use of ISWCHM to prepare geopolymers can simultaneously utilize solid waste resources and solidify heavy metals. In this paper, the latest research progress in the preparation of geopolymers from ISWCHM is reviewed, including the preparation techniques, application and solidification/stabilization mechanisms of heavy metals. In addition, we analyze existing research problems and provide an outlook on future research and development directions.
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| 9. |
- Zhang, Qian, et al.
(author)
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Preparation and hydration of industrial solid waste—cement blends: A review
- 2022
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In: International Journal of Minerals, Metallurgy and Materials. - : Springer Science and Business Media LLC. - 1869-103X .- 1674-4799. ; 29:12, s. 2106-2116
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Research review (peer-reviewed)abstract
- Industrial solid waste (ISW)—cement blends have the advantages of low carbon, low energy consumption, and low pollution, but their clinker replacement level in low carbon cement is generally low. To address this challenge, this study considers the latest progress and development trends in the ISW—cement blend research, focusing on the activation of ISWs, the formation of ISW—cement blends, and their associated hydration mechanisms. After the mechanical activation of ISWs, the D50 (average size) typically drops below 10 µm, and the specific surface area increases above 350 m2/kg. Thermal activation can increase the glassy-phase content and reactivity of ISWs, where the coal gangue activation temperature is usually set at 400–1000°C. Furthermore, the roles of ISWs in the hydration of ISW—cement blends are divided into physical and chemical roles. The physical action of ISWs usually acts in the early stage of the hydration of ISW—cement blends. Subsequently, ISWs participate in the hydration reaction of ISW—cement blends to generate products, such as C—(A)—S—H gels. Moreover, alkali activation affects the hydration kinetics of ISW—cement blends and modifies the proportion of gels. Environmental impacts and costs of ISW—cement blends have also been discussed to guide stakeholders in selecting sustainable ISWs.
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