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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- 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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| 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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- Xin, Yan-Bo, et al.
(författare)
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Research progress of hydrogen tunneling in two-dimensional materials
- 2017
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Ingår i: Wuli xuebao. - : CHINESE PHYSICAL SOC. - 1000-3290. ; 66:5
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Forskningsöversikt (refereegranskat)abstract
- One-atom-thick material such as graphene, graphene derivatives and graphene-like materials, usually has a dense network lattice structure and therefore dense distribution of electronic clouds in the atomic plane. This unique structure makes it have great significance in both basic research and practical applications. Studies have shown that molecules, atoms and ions are very difficult to permeate through these above-mentioned two-dimensional materials. Theoretical investigations demonstrate that even hydrogen, the smallest in atoms, is expected to take billions of years to penetrate through the dense electronic cloud of graphene. Therefore, it is generally considered that one-atom-thin materialis impermeable for hydrogen. However, recent experimental results have shown that the hydrogen atoms can tunnel through graphene and monolayer hexagonal boron nitride at room temperature. The existence of defects in one-atomthin material can also effectively reduce the barrier height of the hydrogen tunneling through graphene. Controversy exists about whether hydrogen particles such as atoms, ions or hydrogen molecules can tunnel through two-dimensional materials, and it has been one of the popular topics in the fields of two-dimensional materials. In this paper, the recent research progressof hydrogen tunneling through two-dimensional materials is reviewed. The characteristics of hydrogen isotopes tunneling through different two-dimensional materials are introduced. Barrier heights of hydrogen tunneling through different graphene and graphene-like materials are discussed and the difficulties in its transition are compared. Hydrogen cannot tunnel through the monolayer molybdenum disulfide, only a little small number of hydrogen atoms can tunnel hrough graphene and hexagonal boron nitride, while hydrogen is relatively easy to tunnel through silicene and phosphorene. The introduction of atomic defects or some oxygen-containing functional groups into the two-dimensional material is discussed, which can effectively reduce the barrier height of the hydrogen tunneling barrier. By adding the catalyst and adjusting the temperature and humidity of the tunneling environment, the hydrogen tunneling ability can be enhanced and the hydrogen particles tunneling through the two-dimensional material can be realized. Finally, the applications of hydrogen tunneling through two-dimensional materials in ion-separation membranes, fuel cells and hydrogen storage materials are summarized. The potential applications of hydrogen permeable functional thin film materials, lithium ion battery electrode materials and nano-channel ions in low energy transmission are prospected. The exact mechanism of hydrogen tunneling through two-dimensional material is yet to be unravelled. In order to promote these applications and to realize large-scale production and precision machining of these two-dimensional materials, an in-depth understanding of the fundamental questions of the hydrogen tunneling mechanism is needed. Further studies are needed to predict the tunneling process quantitatively and to understand the effects of catalyst and the influences of chemical environments.
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| 6. |
- Yu, Zheng Lin, et al.
(författare)
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Environmental water flow can boost foraging success of the juvenile rapa whelk Rapana venosa (Muricidae) in aquaculture tanks with still or flowing water : Indication of chemosensory foraging
- 2019
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486. ; 513
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Tidskriftsartikel (refereegranskat)abstract
- Artificial breeding of Rapana venosa has been attempted in China, but the high mortality rate of rapa whelk juveniles (10–40 mm) seriously restricts the breeding success of this species in artificial cultivation and the overall aquaculture industry, and thus the scale of industrialization is far from being realized. One main factor was found to contribute to this high mortality rate: the low predation efficiency of juveniles. We studied the foraging behavior of various sized R. venosa juveniles in still, flowing, and circulating water, with the juveniles being positioned either upstream or downstream from the prey in the flowing water experiments. Our findings demonstrated that the distance between juveniles and prey in still water significantly restricted the ability of juveniles to locate food, but water flow significantly enhanced this ability. In addition, the small-sized juveniles were found to be more active predators than the larger sized juveniles. Our findings demonstrated that circulating water flow is important to improve the survival and growth rate of juveniles in R. venosa cultures. Our results broaden the understanding of chemical orientation in gastropods and can be used to develop or improve commercial breeding strategies for R. venosa.
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| 7. |
- Yang, Mei Jie, et al.
(författare)
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Expression and activity of critical digestive enzymes during early larval development of the veined rapa whelk, Rapana venosa (Valenciennes, 1846)
- 2020
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486. ; 519
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Tidskriftsartikel (refereegranskat)abstract
- Metamorphosis is a vital developmental event in the life cycle of molluscs and involves extensive morphological and physiological changes. Remodeling of the digestive system is suggested to occur anticipatorily to enable the larva to shift its diet (from filter feeding on microalgae to feeding on small bivalves) after metamorphosis. Changes in the profiles and activities of digestive enzymes, the main executors of digestion, can reflect substantial remodeling of the digestive system. Artificial aquaculture of Rapana venosa, an important commercial shellfish in China, has been hampered because the transition of its food habit during metamorphosis makes determining the timing and dose for bait regulation difficult. In the present study, full-length cDNA sequences encoding cellulase and trypsin were characterized, and cellulase and trypsin mRNA expression levels were analyzed. Additionally, patterns in the activities of six digestive enzymes, including trypsin and cellulase, were investigated throughout the early developmental stage of R. venosa. In the present study, the full-length cDNA of the cellulase gene, comprising 2,086 bp, was found to contain a 1,719-bp open reading frame encoding 572 amino acids, and the full-length cDNA of the trypsin gene was found to be 1,587 bp in length and contained an 855-bp open reading frame encoding 284 amino acids. Quantitative real-time PCR showed that the cellulase levels in R. venosa increased beginning at the early intramembrane veliger stage, whereas cellulase activity was significantly increased in the one-spiral whorl stage. The mRNA expression and activity of trypsin were greatly increased in the juvenile stage (postlarva), whereas those of cellulase were decreased during this stage, which indicated functional changes in the digestive system during larval food habit transition. Our results showed that remodeling of the digestive system occurs prior to metamorphosis and suggest that animal bait should be provided as early as possible to R. venosa in the four-spiral whorl stage to meet its nutritional requirements for the development of its digestive system and to ensure successful metamorphosis of competent larvae.
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