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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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| 4. |
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| 5. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 6. |
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| 7. |
- 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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| 8. |
- Liu, Wei, et al.
(författare)
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Coherent dynamics of multi-spin V-B(-) center in hexagonal boron nitride
- 2022
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Ingår i: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Hexagonal boron nitride (hBN) has recently been demonstrated to contain optically polarized and detected electron spins that can be utilized for implementing qubits and quantum sensors in nanolayered-devices. Understanding the coherent dynamics ofmicrowave driven spins in hBN is of crucial importance for advancing these emerging new technologies. Here, we demonstrate and study the Rabi oscillation and related phenomena of a negatively charged boron vacancy (V-B(-)) spin ensemble in hBN. We report on different dynamics of the V-B(-) spins at weak and strong magnetic fields. In the former case the defect behaves like a single electron spin system, while in the latter case it behaves like a multi-spin system exhibiting multiple-frequency dynamical oscillation as beat in the Ramsey fringes. We also carry out theoretical simulations for the spin dynamics of V-B(-) and reveal that the nuclear spins can be driven via the strong electron nuclear coupling existing in V-B(-) center, which can be modulated by the magnetic field and microwave field.
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| 9. |
- Qu, Luo-Yuan, et al.
(författare)
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Chromatic interferometry with small frequency differences
- 2020
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Ingår i: Optics Express. - 1094-4087. ; 28:22, s. 32294-32301
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Tidskriftsartikel (refereegranskat)abstract
- By developing a 'two-crystal' method for color erasure, we can broaden the scope of chromatic interferometry to include optical photons whose frequency difference falls outside of the 400 nm to 4500 nm wavelength range, which is the passband of a PPLN crystal. We demonstrate this possibility experimentally, by observing interference patterns between sources at 1064.4 nm and 1063.6 nm, corresponding to a frequency difference of about 200 GHz.
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| 10. |
- Zhao, Yan, et al.
(författare)
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Holocene peatland initiation, lateral expansion, and carbon dynamics in the Zoige Basin of the eastern Tibetan Plateau
- 2014
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 24:9, s. 1137-1145
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Tidskriftsartikel (refereegranskat)abstract
- The Zoige Basin on the eastern Tibetan Plateau has the largest area of highland peatlands in China. However, the development history of these peatlands is still poorly understood. Understanding how these carbon-rich ecosystems responded to change in the Asian summer monsoons during the Holocene will provide insight into the peatland carbon accumulation processes under different climate boundary conditions. Here, we document the timing of initiation and expansion histories of these peatlands using 59 new basal peat ages across the Zoige Basin, with 29 ages for initiation analysis and 30 additional ages for lateral expansion analysis. Also, we synthesized basal ages from 26 sites and carbon accumulation records at four sites from previous studies in this region. The results show that the peatland initiation is widespread at 11.5-10 and 7-6 kyr (1 kyr = 1000 cal. yr BP) and the minimum initiation periods occurred after 5 kyr. Our multiple basal ages along eight transects show that slopes are a dominant control on peatland lateral expansion rates, with very slow and less variable rates at slopes >0.4 degrees. Furthermore, we found a significant relationship between peatland basal ages and peat depths from 85 sites, suggesting relatively uniform peat properties. Carbon accumulation rates from detailed downcore analysis at four sites and on the basis of peat depth-basal age relationship show similar patterns with a peak carbon accumulation at 10-8 kyr. On the basis of estimated mean values of bulk density and carbon content from the region, the Holocene average C accumulation for the Zoige Basin is 31.1 g C/m(2)/yr. The widespread peatland initiation and rapid accumulation in the early Holocene were likely in response to higher temperature and stronger summer monsoon intensity, while the slowdown of peatland development during the late Holocene might have been caused by climate cooling and drying.
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