| 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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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Kan, Siyi, et al.
(författare)
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Risk of intact forest landscape loss goes beyond global agricultural supply chains
- 2023
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Ingår i: One Earth. - : Elsevier BV. - 2590-3322 .- 2590-3330. ; 6:1, s. 55-65
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Tidskriftsartikel (refereegranskat)abstract
- The continued loss of unfragmented intact forest landscapes (IFLs) despite numerous global conservation initiatives indicates the need for improved knowledge of proximate and underlying drivers. Yet the role of non-agricultural activities in forest degradation and fragmentation has not received adequate attention. We focus on IFL loss caused by various economic activities and investigate the influence of global consumption and trade via the multi-regional input-output model. For IFL loss associated with the 2014 world economy, over 60% was related to final consumption of non-agricultural products. More than one-third of IFL loss was linked to export, primarily from Russia, Canada, and tropical regions to mainland China, the EU, and the United States. Of IFL loss associated with export, 51% and 26% was directly caused by logging and mining or energy extraction, respectively. The dispersed nature of IFL loss drivers and their indirect links to individual final consumers call for stronger government engagement and supply chain interventions.
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| 4. |
- Li, Xiaowei, 1986, et al.
(författare)
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Metabolic network remodelling enhances yeast’s fitness on xylose using aerobic glycolysis
- 2021
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Ingår i: Nature Catalysis. - : Springer Science and Business Media LLC. - 2520-1158. ; 4:9, s. 783-796
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Tidskriftsartikel (refereegranskat)abstract
- The reprogramming of metabolism in response to switching the carbon source from glucose to non-preferred carbon sources is well-studied for yeast. However, understanding how metabolic networks respond to utilize a non-natural carbon source such as xylose is limited due to the incomplete knowledge of cellular response mechanisms. Here we applied a combination of metabolic engineering, systems biology and adaptive laboratory evolution to gain insights into how yeast can perform a global rewiring of cellular processes to efficiently accompany metabolic transitions. Through metabolic engineering, we substantially enhanced the cell growth on xylose after the growth on glucose. Transcriptome analysis of the engineered strains demonstrated that multiple pathways were involved in the cellular reprogramming. Through genome resequencing of the evolved strains and reverse engineering, we further identified that SWI/SNF chromatin remodelling, osmotic response and aldehyde reductase were responsible for the improved growth. Combined, our analysis showed that glycerol-3-phosphate and xylitol serve as two key metabolites that affect cellular adaptation to growth on xylose. [Figure not available: see fulltext.].
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| 5. |
- Lu, Xiang, et al.
(författare)
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Fine-Granularity Bandwidth Allocation for Diverse Low-Latency Services in Higher-Speed Passive Optical Networks
- 2022
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Ingår i: Asia Communications and Photonics Conference, ACP. - 2162-108X. ; 2022-November, s. 1135-1139
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Konferensbidrag (refereegranskat)abstract
- To support time-sensitive (TS) services with differential low latency requirements, this paper proposes a fine-granularity bandwidth allocation algorithm (FgBA) in higher speed passive optical networks (i.e., ITU-T 50G PON). Simulation results show that FgBA can meet the diverse low latency requirements of TS services regardless of traffic load.
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| 6. |
- Qin, Ning, 1990, et al.
(författare)
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Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast
- 2023
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 186:4, s. 748-763.e15
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Tidskriftsartikel (refereegranskat)abstract
- Although many prokaryotes have glycolysis alternatives, it's considered as the only energy-generating glucose catabolic pathway in eukaryotes. Here, we managed to create a hybrid-glycolysis yeast. Subsequently, we identified an inositol pyrophosphatase encoded by OCA5 that could regulate glycolysis and respiration by adjusting 5-diphosphoinositol 1,2,3,4,6-pentakisphosphate (5-InsP7) levels. 5-InsP7 levels could regulate the expression of genes involved in glycolysis and respiration, representing a global mechanism that could sense ATP levels and regulate central carbon metabolism. The hybrid-glycolysis yeast did not produce ethanol during growth under excess glucose and could produce 2.68 g/L free fatty acids, which is the highest reported production in shake flask of Saccharomyces cerevisiae. This study demonstrated the significance of hybrid-glycolysis yeast and determined Oca5 as an inositol pyrophosphatase controlling the balance between glycolysis and respiration, which may shed light on the role of inositol pyrophosphates in regulating eukaryotic metabolism.
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| 7. |
- Wei, Xinshui, et al.
(författare)
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Delay-aware Rate Adjusting Scheme in Higher Speed Passive Optical Networks
- 2022
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Ingår i: Asia Communications and Photonics Conference, ACP. - 2162-108X. ; 2022-November, s. 1271-1274
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Konferensbidrag (refereegranskat)abstract
- Flexible rate is a new desirable operational feature of next-generation higher speed passive optical networks (e.g., ITU-50G PON). In this context, this paper proposes a delay-aware rate adjusting scheme, in which the line rate can be adjusted following the traffic load varying to save energy without degrading delay performance. Simulation results show that the proposed scheme has a similar performance with the benchmark in the aspect of energy saving, while the delay performance of time-sensitive services can be improved significantly, which can be up to 36%.
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| 8. |
- Bi, Meihua, et al.
(författare)
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Client scheduling and bandwidth slicing for multiple federated learning tasks over multiple passive optical networks
- 2024
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Ingår i: Computer Networks. - 1389-1286. ; 243
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Tidskriftsartikel (refereegranskat)abstract
- Federated Learning (FL) has attracted extensive attention in facilitating emerging edge intelligence applications for its inherent advantages of ensuring data security and privacy. Especially in the edge computing networks connected by Passive Optical Network (PON) system, FL is introduced to enable applications like autonomous driving, intelligent manufacturing, and precision medicine. However, in this system, the FL deployment over PON inevitably faces challenges induced by the conflict between a large volume of model data with the restrict latency limitation and the confined bandwidth resource of PON, especially for the multiple FL tasks. To address these issues, a novel scheme is proposed for tackling the client distribution and bandwidth allocation problems under the scenario of multiple simultaneous FL tasks supported by the multiple interconnected PON systems, which is consisted of the client scheduling and bandwidth slicing processes. To be specific, an easy-to-implement heuristic algorithm is first performed to assign the client numbers to PONs based on iterative method, with which certain operations are repetitively executed to achieve optimal solutions. And then, the serial bandwidth slicing which adapts the traditional policy, i.e., one-task-per-cycle, to the situation with multiple FL tasks, and parallel slicing with the multi-task-per-cycle, are designed for the investigated system. Furthermore, the simulation system is constructed to verify our method. The corresponding results exhibit that, the largest 43.2 % round time reduction is achieved by client scheduling compared to benchmark without the scheduling. Compared to the benchmark with serial slicing, our scheme can achieve a maximum 50.11 % of the round time decrease. It's also validated that, our proposed client scheduling and parallel bandwidth slicing method can improve the learning efficiency by reducing communication delay, especially for the situation with less client number and smaller FL threshold.
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| 9. |
- Cao, Yuan, et al.
(författare)
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Hybrid Trusted/Untrusted Relay Based Quantum Key Distribution over Optical Backbone Networks
- 2021
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Ingår i: IEEE Journal on Selected Areas in Communications. - 0733-8716 .- 1558-0008. ; 39:9, s. 2701-2718
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Tidskriftsartikel (refereegranskat)abstract
- Quantum key distribution (QKD) has demonstrated a great potential to provide future-proofed security, especially for 5G and beyond communications. As the critical infrastructure for 5G and beyond communications, optical networks can offer a cost-effective solution to QKD deployment utilizing the existing fiber resources. In particular, measurement-device-independent QKD shows its ability to extend the secure distance with the aid of an untrusted relay. Compared to the trusted relay, the untrusted relay has obviously better security, since it does not rely on any assumption on measurement and even allows to be accessed by an eavesdropper. However, it cannot extend QKD to an arbitrary distance like the trusted relay, such that it is expected to be combined with the trusted relay for large-scale QKD deployment. In this work, we study the hybrid trusted/untrusted relay based QKD deployment over optical backbone networks and focus on cost optimization during the deployment phase. A new network architecture of hybrid trusted/untrusted relay based QKD over optical backbone networks is described, where the node structures of the trusted relay and untrusted relay are elaborated. The corresponding network, cost, and security models are formulated. To optimize the deployment cost, an integer linear programming model and a heuristic algorithm are designed. Numerical simulations verify that the cost-optimized design can significantly outperform the benchmark algorithm in terms of deployment cost and security level. Up to 25% cost saving can be achieved by deploying QKD with the hybrid trusted/untrusted relay scheme while keeping much higher security level relative to the conventional point-to-point QKD protocols that are only with the trusted relays.
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| 10. |
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