| 1. |
- 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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| 2. |
- Cao, Zhixing, et al.
(författare)
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Multi-scale data-driven engineering for biosynthetic titer improvement
- 2020
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Ingår i: Current Opinion in Biotechnology. - : Elsevier BV. - 0958-1669 .- 1879-0429. ; 65, s. 205-212
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Forskningsöversikt (refereegranskat)abstract
- Industrial biosynthesis is a very complex process which depends on a range of different factors, from intracellular genes and metabolites, to extracellular culturing conditions and bioreactor engineering. The identification of species that improve the titer of some reaction is akin to the task of finding a needle in a haystack. This review aims to summarize state-of-the-art biosynthesis titer improvement on different scales separately, particularly regarding the advancement of metabolic pathway rewiring and data-driven process optimization and control. By integrating multi-scale data and establishing a mathematical replica of a real biosynthesis, more refined quantitative insights can be gained for achieving a higher titer than ever.
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| 3. |
- Zhang, Li, et al.
(författare)
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Characterization of anti-BCG benz[α]anthraquinones and new siderophores from a Xinjiang desert-isolated rare actinomycete Nocardia sp. XJ31
- 2020
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Ingår i: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 104:19, s. 8267-8278
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Tidskriftsartikel (refereegranskat)abstract
- The current global demand for novel anti-TB drugs has drawn urgent attention on the discovery of natural product compounds with anti-TB activity. Lots of efforts have emphasized on environmental samples from unexplored or underexplored natural habits and identified numerous rare actinomycete taxa producing structurally diverse bioactive natural products. Herein, we report a survey of the rare actinobacteria diversity in Xinjiang region together with the discovery of anti-TB active natural products from these strains. We have collected 17 soil samples at different sites with different environmental conditions, from which 39 rare actinobacteria were identified by using a selective isolation strategy with 5 media variations. Among those isolated strains, XJ31 was identified as a new Nocardia sp. based on 16S rRNA gene analysis. Through one strain-many compounds (OSMAC) strategy combined with anti-Bacillus Calmette-Guérin bioassay-guided isolation, two groups of compounds were identified. They were twelve siderophores (nocardimicins, 1-12) and two anthraquinones (brasiliquinones, 13 and 14) and ten of them were identified as new compounds. The structures of the purified compounds were elucidated using HR-ESI-MS, 1D NMR, and 2D NMR techniques. The anti-TB bioassays revealed that the two benz[α]anthraquinones have potent activity against BCG (MICs = 25 μM), which can be used as a promising start point for further anti-TB drug development.
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| 4. |
- Chang, Y. S., et al.
(författare)
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Extending on-chip interconnects for rack-level remote resource access
- 2016
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Ingår i: Proceedings of the 34th IEEE International Conference on Computer Design, ICCD 2016. - 1063-6404. - 9781509051427 ; , s. 56-63
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Konferensbidrag (refereegranskat)abstract
- The need to perform data analytics on exploding data volumes coupled with the rapidly changing workloads in cloud computing places great pressure on data-center servers. To improve hardware resource utilization across servers within a rack, we propose Direct Extension of On-chip Interconnects (DEOI), a high-performance and efficient architecture for remote resource access among server nodes. DEOI extends an SoC server node's on-chip interconnect to access resources in adjacent nodes with no protocol changes, allowing remote memory and network resources to be used as if they were local. Our results on a four-node FPGA prototype show that the latency of user-level, cross-node, random reads to DEOI-connected remote memory is as low as 1.16?s, which beats current commercial technologies. We exploit DEOI remote access to improve performance of the Redis in-memory key-value framework by 47%. When using DEOI to access remote network resources, we observe an 8.4% average performance degradation and only a 2.52?s ping-pong latency disparity compared to using local assets. These results suggest that DEOI can be a promising mechanism for increasing both performance and efficiency in next-generation data-center servers.
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| 5. |
- Chen, Youchun, et al.
(författare)
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Insights into the working mechanism of cathode interlayers in polymer solar cells via [(C8H17)(4)N](4)[SiW12O40]
- 2016
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Ingår i: Journal of Materials Chemistry A. - : ROYAL SOC CHEMISTRY. - 2050-7488 .- 2050-7496. ; 4:48, s. 19189-19196
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Tidskriftsartikel (refereegranskat)abstract
- A low-cost (amp;lt;$1 per g), high-yield (amp;gt;90%), alcohol soluble surfactant-encapsulated polyoxometalate complex [(C8H17)(4)N](4)[SiW12O40] has been synthesized and utilized as a cathode interlayer (CIL) in polymer solar cells (PSCs). A power conversion efficiency of 10.1% can be obtained for PSCs based on PTB7-Th (poly[[2,6-4,8-di(5-ethylhexylthienyl) benzo[1,2-b;3,3-b]-dithiophene][3-fluoro-2[(2-ethylhexyl) carbonyl] thieno [3,4-b]-thiophenediyl]]):PC71BM ([6,6]-phenyl C71-butyric acidmethyl ester) due to the incorporation of [(C8H17)(4)N](4)[SiW12O40]. Combined measurements of current density-voltage characteristics, transient photocurrent, charge carrier mobility and capacitance-voltage characteristics demonstrate that [(C8H17)(4)N](4)[SiW12O40] can effectively increase the built-in potential, charge carrier density and mobility and accelerate the charge carrier extraction in PSCs. Most importantly, the mechanism of using [(C8H17)(4)N](4)[SiW12O40] as the CIL is further brought to light by X-ray photoemission spectroscopy (XPS) and ultraviolet photoemission spectroscopy (UPS) of the metal/ [(C8H17)(4)N](4)[SiW12O40] interface. The findings suggest that [(C8H17)(4)N](4)[SiW12O40] not only decreased the work function of the metal cathodes but also was n-doped upon contact with the metals, which provide insights into the working mechanism of the CILs simultaneously improving the open circuit voltage, short circuit current and fill factor in the PSCs.
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| 6. |
- Jiang, Lan, et al.
(författare)
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Heparin mimetics as potential intervention for COVID-19 and their bio-manufacturing
- 2023
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Ingår i: SYNTHETIC AND SYSTEMS BIOTECHNOLOGY. - : KEAI PUBLISHING LTD. - 2405-805X. ; 8:1, s. 11-19
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Forskningsöversikt (refereegranskat)abstract
- The COVID-19 pandemic has caused severe health problems worldwide and unprecedented decimation of the global economy. Moreover, after more than 2 years, many populations are still under pressure of infection. Thus, a broader perspective in developing antiviral strategies is still of great importance. Inspired by the observed multiple benefits of heparin in the treatment of thrombosis, the potential of low molecular weight heparin (LMWH) for the treatment of COVID-19 have been explored. Clinical applications found that LMWH decreased the level of inflammatory cytokines in COVID-19 patients, accordingly reducing lethality. Furthermore, several in vitro studies have demonstrated the important roles of heparan sulfate in SARS-CoV-2 infection and the inhibitory effects of heparin and heparin mimetics in viral infection. These clinical observations and designed studies argue for the potential to develop heparin mimetics as anti-SARS-CoV-2 drug candidates. In this review, we summarize the properties of heparin as an anticoagulant and the pharmaceutical possibilities for the treatment of virus infection, focusing on the perspectives of developing heparin mimetics via chemical synthesis, chemoenzymatic synthesis, and bioengineered production by microbial cell factories. The ultimate goal is to pave the eminent need for exploring novel compounds to treat coronavirus infection-caused diseases.
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| 7. |
- Qiao, Lixin, et al.
(författare)
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Solid Polymer Electrolytes Comprising Camphor-Derived Chiral Salts for Solid-State Batteries
- 2020
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Ingår i: Journal of the Electrochemical Society. - : The Electrochemical Society. - 1945-7111 .- 0013-4651. ; 167:12
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Tidskriftsartikel (refereegranskat)abstract
- Solid polymer electrolytes (SPEs) with both excellent processability and flexibility have been deemed as an auspicious alternative to develop safe solid-state lithium metal (Li°) batteries (SSLMBs). The electrochemical performance of SSLMBs is ultimately associated with the nature of the Li-salt anion and the widely used bis(trifluoromethanesulfonyl)imide anion (TFSI) is "slippery"due to its perfluorinated nature and therefore highly mobile, which leads to severe polarization upon battery cell charge/discharge cycles. In this work, we report on a new type of chiral salts, synthesized from commercially available camphorsulfonic acid, used in poly(ethylene oxide) (PEO)-based SPEs. The impact of the chirality of the anions on the fundamental physical properties of the SPEs is extensively studied in terms of thermal stability, phase transition and ionic conductivity, etc. We demonstrate that the resulting SPEs exhibit agreeable ionic conductivities (ca. 104 S cm1) accompanied by high cation transference numbers (ca. 0.5) at 70 °C. Whether either the R or the S enantiomers are used the ion transport properties are the same, as expected, but rather surprisingly the artificial racemic mixture is within the errors of the measurements just as conductive. We discuss how this opens a new avenue to design novel salts for reaching high-performant SSLMBs.
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| 8. |
- Sun, Yong, et al.
(författare)
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Decomposition of physical processes controlling EASM precipitation changes during the mid-Piacenzian : new insights into data–model integration
- 2024
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Ingår i: npj Climate and Atmospheric Science. - 2397-3722. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- The mid-Piacenzian warm period (MPWP, ~3.264–3.025 Ma) has gained widespread interest due to its partial analogy with future climate. However, quantitative data–model comparison of East Asian Summer Monsoon (EASM) precipitation during the MPWP is relatively rare, especially due to problems in decoding the imprint of physical processes to climate signals in the records. In this study, pollen-based precipitation records are reconstructed and compared to the multi-model ensemble mean of the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). We find spatially consistent precipitation increase in most simulations but a spatially divergent change in MPWP records. We reconcile proxy data and simulation by decomposing physical processes that control precipitation. Our results 1) reveal thermodynamic control of an overall enhancement of EASM precipitation and 2) highlight a distinct control of thermodynamic and dynamical processes on increases of tropical and subtropical EASM precipitation, reflecting the two pathways of water vapor supply that enhance EASM precipitation, respectively.
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| 9. |
- Zhang, Chengyu, et al.
(författare)
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Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community
- 2024
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Ingår i: Molecular Systems Biology. - 1744-4292. ; In Press
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Tidskriftsartikel (refereegranskat)abstract
- Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This has increased the quality and scope of the model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or reference conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference for nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains’ growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine learning models. Based on those findings we anticipate that Yeast9 will continue to empower systems biology studies of yeast metabolism.
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| 10. |
- Zhang, Liuhang, et al.
(författare)
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P-Socket: Optimizing a communication library for a PCIe-based intra-rack interconnect
- 2016
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Ingår i: ACM International Conference on Computing Frontiers, CF 2016; Como; Italy; 16 May 2016 through 18 May 2016. - New York, NY, USA : ACM. - 9781450341288 ; , s. 145-153
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Konferensbidrag (refereegranskat)abstract
- Data centers require efficient, low-cost, exible interconnects to manage the rapidly growing internal traffic generated by an increasingly diverse set of applications. To meet these re-quirements, data center networks are increasingly employing alternatives such as RapidIO, Freedom, and PCIe, which re-quire fewer physical devices and/or have simpler protocols than more traditional interconnects. These networks offer raw high performance communication capabilities, but sim-ply using them for conventional TCP/IP-based communica-tion fails to realize the potential performance of the physical network. Here we analyze causes for this performance loss for the TCP/IP protocol over one such fabric, PCIe, and we explore a hardware/software solution that mitigates over-heads and exploits PCIe's advanced features. The result is P-Socket, an efficient library that enables legacy socket applications to run without modification. Our experiments show that P-Socket achieves an end-To-end latency of 1.2s and effiective bandwidth of up to 2.87GB/s (out of a theo-retical peak of 3.05GB/s).
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