| 1. |
|
|
| 2. |
- Beal, Jacob, et al.
(author)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)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.
|
|
| 3. |
|
|
| 4. |
- Klionsky, Daniel J., et al.
(author)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Research review (peer-reviewed)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.
|
|
| 5. |
- Xiao, Tian, et al.
(author)
-
Numerical study of heat transfer and load-bearing performances of corrugated sandwich structure with open-cell metal foam
- 2023
-
In: International Journal of Heat and Mass Transfer. - 0017-9310. ; 215
-
Journal article (peer-reviewed)abstract
- Critical engineering applications require lightweight components that can effectively dissipate heat and provide sufficient load-bearing capacity. Examples of such applications include the jet blast deflector (JBD) on an aircraft carrier and engine combustion chambers in supersonic vehicles. While lightweight corrugated sandwich structures (CSSs) exhibit excellent load-bearing capacity, their heat transfer capacity falls short. To overcome this limitation, a strategy of filling the CSS with an open-cell metal foam (MF) is proposed to create a sandwich structure with ultralight load bearing and heat transfer capabilities. Numerical simulations were conducted to study the heat transfer and load-bearing performance of this new structure. The findings indicate that the use of a MF significantly improves the heat transfer capabilities of the CSS. Compared to the CSS, the Nusselt number of MF and CSS-foam composite at a Reynolds number of 240 were enhanced by 51.3% and 102.3%, respectively. The overall thermal performance of CSS-foam composites was optimized under the same pumping power constraints. In turbulent conditions, the overall thermal performance of CSS-foam composites was 5.9% to 55.4% higher than that of CSS in turbulent conditions. Furthermore, the simulations showed that when the CSS was subjected to static and quasi-static compression, the maximum von Mises stress occurred at the connection between the panel and the web.
|
|
| 6. |
|
|
| 7. |
- Ai, Yue-Jie, et al.
(author)
-
Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein
- 2013
-
In: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 111:9-11, s. 1316-1321
-
Journal article (peer-reviewed)abstract
- Two-photon absorption spectra of green fluorescent proteins (GFPs) often show a blue-shift band compared to their conventional one-photon absorption spectra, which is an intriguing feature that has not been well understood. We present here a systematic study on one- and two-photon spectra of GFP chromophore by means of the density functional response theory and complete active space self-consistent field (CASSCF) methods. It shows that the popular density functional fails to provide correct vibrational progression for the spectra. The non-Condon vibronic coupling, through the localised intrinsic vibrational modes of the chromophore, is responsible for the blue-shift in the TPA spectra. The cis to trans isomerisation can be identified in high-resolution TPA spectra. Our calculations demonstrate that the high level ab initio multiconfigurational CASSCF method, rather than the conventional density functional theory is required for investigating the essential excited-state properties of the GFP chromophore.
|
|
| 8. |
|
|
| 9. |
- Cai, Xuelian, et al.
(author)
-
Safety-Oriented Personalized Service Strategy in Air-Ground Integrated Mobility
- 2024
-
In: IEEE Transactions on Vehicular Technology. - 0018-9545 .- 1939-9359. ; 73:2, s. 2564-2577
-
Journal article (peer-reviewed)abstract
- Air-ground Integrated Mobility (AIM) can effectively alleviate the current urban traffic pressure by expanding transportation resources in the near-ground field. However, the following problems in AIM need to be addressed urgently: 1) The high mobility of Personal Aerial Vehicles (PAVs) in low-altitude airspace leads to a sharp increase in risk factors; 2) Due to the limited communication distance, antenna direction angle, and frequent handover caused by high-speed movement, the communication quality in the air is unreliable; 3) AIM incorporates vehicles on the ground and PAVs in the air leading to the high variability of user requirements. Confronted with the personalized resource requirements of high-speed mobile PAVs in airspace with unreliable communication quality, traditional resource allocation strategies struggle to guarantee service quality. Therefore, we propose a safety-oriented personalized resource allocation strategy in AIM, which jointly considers the user requirements and resource distribution. Specifically, we first build a three-dimensional (3D) safety distance model by analyzing the motion process of PAVs with the help of a kinematics model. Then, according to the location, speed, and environmental information of the PAVs, the communication and computing resources required by each PAV under the premise of maintaining the optimal safety distance are obtained through the transmission model. Furthermore, the 3D safety distance and resources are jointly optimized, and an on-demand resource allocation algorithm enabled by Deep Reinforcement Learning (DRL) is constructed to provide the resource allocation strategy based on the personalized requirements of the users.
|
|
| 10. |
- Chen, Yue, et al.
(author)
-
A novel nanoparticle system targeting damaged mitochondria for the treatment of Parkinson's disease
- 2022
-
In: Biomaterials Advances. - : Elsevier BV. - 2772-9516 .- 2772-9508. ; 138
-
Journal article (peer-reviewed)abstract
- Mitochondrial damage is one of the primary causes of neuronal cell death in Parkinson's disease (PD). In PD patients, the mitochondrial damage can be repaired or irreversible. Therefore, mitochondrial damage repair becomes a promising strategy for PD treatment. In this research, hyaluronic acid nanoparticles (HA-NPs) of different molecular weights are used to protect the mitochondria and salvage the mild and limited damage in mitochondria. The HA-NPs with 2190 k Dalton (kDa) HA can improve the mitochondrial function of SH-SY5Y cells and PTEN induced putative kinase 1 (PINK1) knockout mouse embryo fibroblast (MEF) cells. In cases of irreversible damage, NPs with ubiquitin specific peptidase 30 (USP30) siRNA are used to promote mitophagy. Meanwhile, by adding PINK1 antibodies, the NPs can selectively target the irreversibly damaged mitochondria, preventing the excessive clearance of healthy mitochondria.
|
|
