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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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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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| 6. |
- Nie, Shuai, et al.
(författare)
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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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Ingår i: Horticulture Research. - : Oxford University Press. - 2662-6810 .- 2052-7276. ; 10:1
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Tidskriftsartikel (refereegranskat)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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| 7. |
- Nie, Shuai, et al.
(författare)
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Progress in phylogenetics, multi-omics and flower coloration studies in Rhododendron
- 2024
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Ingår i: Ornamental Plant Research. - : Maximum Academic Press. - 2769-2094. ; 4
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Forskningsöversikt (refereegranskat)abstract
- The genus Rhododendron exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in Rhododendron. We describe advances in phylogenetic reconstruction and genome sequencing of Rhododendron species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the Rhododendron lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.
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| 8. |
- Wang, Yu-Cheng, et al.
(författare)
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Porous Carbon Membrane-Supported Atomically Dispersed Pyrrole-Type Fe-N-4 as Active Sites for Electrochemical Hydrazine Oxidation Reaction
- 2020
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Ingår i: Small. - : Wiley. - 1613-6810 .- 1613-6829. ; 16:31
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Tidskriftsartikel (refereegranskat)abstract
- The rational design of catalytically active sites in porous materials is essential in electrocatalysis. Herein, atomically dispersed Fe-N-x sites supported by hierarchically porous carbon membranes are designed to electrocatalyze the hydrazine oxidation reaction (HzOR), one of the key techniques in electrochemical nitrogen transformation. The high intrinsic catalytic activity of the Fe-N-x single-atom catalyst together with the uniquely mixed micro-/macroporous membrane support positions such an electrode among the best-known heteroatom-based carbon anodes for hydrazine fuel cells. Combined with advanced characterization techniques, electrochemical probe experiments, and density functional theory calculation, the pyrrole-type Fe-N-4 structure is identified as the real catalytic site in HzOR.
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| 9. |
- Xue, Tian-Tian, et al.
(författare)
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Ignored Biodiversity in Acid Soil Islands in Karst Areas, South China : Impatiens longlinensis (Balsaminaceae), a New Critically Endangered Species
- 2020
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Ingår i: Systematic Botany. - 0363-6445 .- 1548-2324. ; 45:4, s. 891-899
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Tidskriftsartikel (refereegranskat)abstract
- The karst area in South China is notable for its fragile vegetation and unique flora with many narrow endemic species, and is one of the most threatened biodiversity hotspots in the world. However, the biodiversity of acid soil areas scattered in the karst area have previously been underestimated. With a recent increase of new discoveries of plants and animals, the conservation of biodiversity in these acid soil areas has become urgent. This study deals with a new species, Impatiens longlinensis . The new species is similar to I. yui and I. lasiophyton in having pubescence, two lateral sepals, funnelform lower sepal, and linear capsule. But it can be distinguished by having orbicular to obovate dorsal sepals and oblong to elliptic lower and upper lobes of lateral united petals. Moreover, molecular data and micro-morphological evidence also support that the species is new to science. The new species is only known from a valley near the summit of Mt. Jinzhongshan within an area of less than 5 km2. Based on the Red List categories and criteria developed by the International Union for Conservation of Nature, and the threat posed by exploitation for tourism development, we categorize it as Critically Endangered (CR).
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| 10. |
- Yang, Fu-Sheng, et al.
(författare)
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Chromosome-level genome assembly of a parent species of widely cultivated azaleas
- 2020
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea. Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.
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