| 1. |
- 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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| 2. |
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| 3. |
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| 4. |
- 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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| 5. |
- Li, Xiaoting, et al.
(författare)
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"Mix-Then-On-Demand-Complex" : In Situ Cascade Anionization and Complexation of Graphene Oxide for High-Performance Nanofiltration Membranes
- 2021
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 15:3, s. 4440-4449
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Tidskriftsartikel (refereegranskat)abstract
- Assembling two-dimensional (2D) materials by polyelectrolyte often suffers from inhomogeneous microstructures due to the conventional mixing-and-simultaneous-complexation procedure (mix-and-complex) in aqueous solution. Herein a mix-then-on-demand-complex concept via on-demand in situ cascade anionization and ionic complexation of 2D materials is raised that drastically improves structural order in 2D assemblies, as exemplified by classical graphene oxide (GO)-based ultrathin membranes. Specifically, in dimethyl sulfoxide, the carboxylic acid-functionalized GO sheets (COOH-GOs) were mixed evenly with a cationic poly(ionic liquid) (PIL) and upon filtration formed a well-ordered layered composite membrane with homogeneous distribution of PIL chains in it; next, whenever needed, it was alkali-treated to convert COOH-GO in situ into its anionized state COO--GO that immediately complexed ionically with the surrounding cationic PIL chains. This mix-then-on-demand-complex concept separates the ionic complexation of GO and polyelectrolytes from their mixing step. By synergistically combining the PIL-induced hydrophobic confinement effect and supramolecular interactions, the as-fabricated nanofiltration membranes carry interface transport nanochannels between GO and PIL, reaching a high water permeability of 96.38 L m(-2) h(-1) bar(-1) at a maintained excellent dye rejection 99.79% for 150 h, exceeding the state-of-the-art GO-based hybrid membranes. The molecular dynamics simulations support the experimental data, confirming the interface spacing between GO and PIL as the water transport channels.
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| 6. |
- Li, Xiaoting, et al.
(författare)
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Nano-confinement-inspired metal organic framework/polymer composite separation membranes
- 2020
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 8:33, s. 17212-17218
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Tidskriftsartikel (refereegranskat)abstract
- A defect-free, robust and selective barrier is essential for manufacturing membranes with targeted high permeability and selectivity. Here we report a new route to engineering a separation composite membrane by confining both channels in nanoscale metal organic frameworks (MOFs) and charges in a polyelectrolyte in the inner space of a porous supportviaa counter-diffusion method. A simple thermal annealing treatment of the interface between the MOF, polymer and support favorably reduced voids inside this nano-confinement environment. As this composite membrane combines both the support and barrier as one, it minimizes mass transfer resistance of water molecules. In a separation test, it readily achieved the state-of-the-art permeance. This simple chemical approach to upgrade membrane structures will offer wide opportunities in separation devices.
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| 7. |
- Lu, Yahua, et al.
(författare)
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Engineer Nanoscale Defects into Selective Channels : MOF-Enhanced Li+ Separation by Porous Layered Double Hydroxide Membrane
- 2023
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Ingår i: Nano-Micro Letters. - 2311-6706. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) membrane-based ion separation technology has been increasingly explored to address the problem of lithium resource shortage, yet it remains a sound challenge to design 2D membranes of high selectivity and permeability for ion separation applications. Zeolitic imidazolate framework functionalized modified layered double hydroxide (ZIF-8@MLDH) composite membranes with high lithium-ion (Li+) permeability and excellent operational stability were obtained in this work by in situ depositing functional ZIF-8 nanoparticles into the nanopores acting as framework defects in MLDH membranes. The defect-rich framework amplified the permeability of Li+, and the site-selective growth of ZIF-8 in the framework defects bettered its selectivity. Specifically speaking, the ZIF-8@MLDH membranes featured a high permeation rate of Li+ up to 1.73 mol m−2 h−1 and a desirable selectivity of Li+/Mg2+ up to 31.9. Simulations supported that the simultaneously enhanced selectivity and permeability of Li+ are attributed to changes in the type of mass transfer channels and the difference in the dehydration capacity of hydrated metal cations when they pass through nanochannels of ZIF-8. This study will inspire the ongoing research of high-performance 2D membranes through the engineering of defects.
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| 8. |
- Lu, Yahua, et al.
(författare)
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Heterostructure membranes of high permeability and stability assembled from MXene and modified layered double hydroxide nanosheets
- 2023
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Ingår i: Journal of Membrane Science. - 0376-7388 .- 1873-3123. ; 688
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Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) MXene-based lamellar membranes play transformative roles in membrane filtration technology. Their practical use in water treatment is however hindered by several hurdles, e.g., unfavorable swelling due to weak interactions between adjacent MXene nanosheets, tortuous diffusion pathways of layered stacking, and the intrinsic aquatic oxidation-prone nature of MXene. Herein, nanoporous 2D/2D heterostructure membranes are elaborately constructed via solution-phase assembly of oppositely charged MXene and modified layered double hydroxide (MLDH) nanosheets. As a multifunctional component, positively charged holey MLDH nanosheets were first tailor-made to serve simultaneously as a binder, spacer and surface-modifier; next they were intercalated into negatively charged MXene lamella to enhance structural stability and mass transfer of membranes. As a result, the as-prepared MLDH@MXene heterostructure membranes successfully break the persistent trade-off between high permeability and selectivity while mitigating the common drawbacks in 2D MXene-based lamellar membranes, e.g., swelling issues, restacking problems, and vulnerable chemical stability. Noticeably, at an operating pressure of 4 bar and a feed solution of 100 ppm of Congo red, the heterostructure membranes enable a threefold jump in permeability (332.7 +/- 20 L m(-2) h(-1 )bar(-1)) when compared to the pristine MXene membrane (119.3 +/- 18 L m(-2 )h(-1) bar(-1)), and better operational stability without compromising the rejection.
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| 9. |
- 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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