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- 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. |
- Xu, Nan, et al.
(författare)
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Global optimization energy management for multi-energy source vehicles based on "Information layer - Physical layer - Energy layer- Dynamic programming" (IPE-DP)
- 2022
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Ingår i: Applied Energy. - : Elsevier BV. - 0306-2619 .- 1872-9118. ; 312
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Tidskriftsartikel (refereegranskat)abstract
- To reveal the energy-saving mechanisms of global energy management, we propose a global optimization framework of "information layer-physical layer-energy layer-dynamic programming " (IPE-DP), which can realize the unity of different information scenarios, different vehicle configurations and energy conversions. The deterministic dynamic programing (DP) and adaptive dynamic programming (ADP) are taken as the core algorithms. As a benchmark for assessing the optimality, DP strategy has four main challenges: standardization, real-time application, accuracy, and satisfactory drivability. To solve the above problems, the IPE-DP optimization framework is established, which consists of three main layers, two interface layers and an application layer. To be specific, the full-factor trip information is acquired from three scenarios in the information layer, and then the feasible work modes of the vehicle are determined in the physical layer based on the proposed conservation framework of "kinetic/potential energy & onboard energy ". The above lays a foundation for the optimal energy distribution in the energy layer. Then, a global domain-searching algorithm and action dependent heuristic dynamic programming (ADHDP) model are developed for different information acquisition scenarios to obtain the optimal solution. To improve the computational efficiency under the deterministic information, a fast DP is developed based on the statistical rules of DP behavior, the core of which is to restrict the exploring region based on a reference SOC trajectory. Regarding the stochastic trip information, the ADHDP model is established, including determining the utility function, network design and training process. Finally, two case studies are given to compare the economic performance of the vehicle under different information acquisition scenarios, which lays a foundation for analyzing the relationship between the amount of information input and energy-saving potential of the vehicle. Simulation results demonstrate that the proposed method gains a better performance in both real-time performance and global optimality.
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| 6. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 9. |
- Li, Cai, et al.
(författare)
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Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment
- 2014
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Ingår i: GigaScience. - 2047-217X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adelie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Results: Phylogenetic dating suggests that early penguins arose similar to 60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from similar to 1 million years ago to similar to 100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Conclusions: Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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| 10. |
- Li, Hailong, 1976-, et al.
(författare)
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A self-powered smart wave energy converter for sustainable sea
- 2024
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Ingår i: Mechanical systems and signal processing. - : Academic Press. - 0888-3270 .- 1096-1216. ; 220
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Tidskriftsartikel (refereegranskat)abstract
- Self-powered smart buoys are widely used in sustainable sea, such as marine environmental monitoring. The article designs a self-powered and self-sensing point-absorber wave energy converter based on the two-arm mechanism. The system consists of the wave energy capture module, the power take-off module, the generator module and the energy storage module. As the core component of the wave energy converter, the power take-off module is mainly composed of a two-arm mechanism, which can convert the oscillation heave motion into unidirectional rotary motion. To evaluate the power generation performance of the system, the kinematic and dynamic models of the wave energy converter with the flywheel are established, and the disengagement and engagement phenomena of the flywheel are analyzed. The effectiveness of the prototype in capturing wave energy is verified through dry experiments in lab and field tests. The dry experiment reveals that the maximum output power of the system is 5.67 W, and the maximum and average mechanical efficiency are 66.63 % and 48.35 %, respectively. Additionally, the field test demonstrates that the peak output power can reach 92 W. Meanwhile, the generated electrical signals can be processed by deep learning algorithms to accurately identify different wave states. This high performance confirms that the proposed wave energy converter can meet its own energy needs by capturing wave energy in the marine environment, while also achieving self-sensing for wave condition monitoring. The system has great potential for promoting the development of intelligent sustainable sea in the future.
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