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| 2. |
- 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. |
- Gao, Xindi, et al.
(författare)
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Cryptococcal Hsf3 controls intramitochondrial ROS homeostasis by regulating the respiratory process
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondrial quality control prevents accumulation of intramitochondrial-derived reactive oxygen species (mtROS), thereby protecting cells against DNA damage, genome instability, and programmed cell death. However, underlying mechanisms are incompletely understood, particularly in fungal species. Here, we show that Cryptococcus neoformans heat shock factor 3 (CnHsf3) exhibits an atypical function in regulating mtROS independent of the unfolded protein response. CnHsf3 acts in nuclei and mitochondria, and nuclear- and mitochondrial-targeting signals are required for its organelle-specific functions. It represses the expression of genes involved in the tricarboxylic acid cycle while promoting expression of genes involved in electron transfer chain. In addition, CnHsf3 responds to multiple intramitochondrial stresses; this response is mediated by oxidation of the cysteine residue on its DNA binding domain, which enhances DNA binding. Our results reveal a function of HSF proteins in regulating mtROS homeostasis that is independent of the unfolded protein response.
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| 4. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 5. |
- Li, Bo, et al.
(författare)
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Therapeutic rationale to target highly expressed CDK7 conferring poor outcomes in triple-negative breast cancer
- 2017
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Ingår i: Cancer Research. - 0008-5472. ; 77:14, s. 3834-3845
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Tidskriftsartikel (refereegranskat)abstract
- Triple-negative breast cancer (TNBC) patients commonly exhibit poor prognosis and high relapse after treatment, but there remains a lack of biomarkers and effective targeted therapies for this disease. Here, we report evidence highlighting the cell-cycle–related kinase CDK7 as a driver and candidate therapeutic target in TNBC. Using publicly available transcriptomic data from a collated set of TNBC patients (n ¼ 383) and the METABRIC TNBC dataset (n ¼ 217), we found CDK7 mRNA levels to be correlated with patient prognosis. High CDK7 protein expression was associated with poor prognosis within the RATHER TNBC cohort (n ¼ 109) and the METABRIC TNBC cohort (n ¼ 203). The highly specific CDK7 kinase inhibitors, BS-181 and THZ1, each downregulated CDK7-mediated phosphorylation of RNA polymerase II, indicative of transcriptional inhibition, with THZ1 exhibiting 500-fold greater potency than BS-181. Mechanistic investigations revealed that the survival of MDA-MB-231 TNBC cells relied heavily on the BCL-2/BCL-XL signaling axes in cells. Accordingly, we found that combining the BCL-2/BCL-XL inhibitors ABT-263/ABT199 with the CDK7 inhibitor THZ1 synergized in producing growth inhibition and apoptosis of human TNBC cells. Collectively, our results highlight elevated CDK7 expression as a candidate biomarker of poor prognosis in TNBC, and they offer a preclinical proof of concept for combining CDK7 and BCL-2/BCL-XL inhibitors as a mechanism-based therapeutic strategy to improve TNBC treatment.
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| 6. |
- Liu, Jian-li, et al.
(författare)
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China's most typical nonferrous organic-metal facilities own specific microbial communities
- 2018
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- The diversity and function of microorganisms have yet to be explored at non-ferrous metal mining facilities (NMMFs), which are the world's largest and potentially most toxic sources of co-existing metal(loid)s and flotation reagents (FRs). The diversity and inferred functions of different bacterial communities inhabiting two types of sites (active and abandoned) in Guangxi province (China) were investigated for the first time. Here we show that the structure and diversity of bacteria correlated with the types of mine sites, metal(loid)s, and FRs concentrations; and best correlated with the combination of pH, Cu, Pb, and Mn. Combined microbial coenobium may play a pivotal role in NMMFs microbial life. Arenimonas, specific in active mine sites and an acidophilic bacterium, carries functions able to cope with the extreme conditions, whereas Latescibacteria specific in abandoned sites can degrade organics. Such a bacterial consortium provides new insights to develop cost-effective remediation strategies of co-contaminated sites that currently remain intractable for bioremediation.
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| 7. |
- Magni, Stefano, et al.
(författare)
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Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data
- 2024
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Ingår i: npj Systems Biology and Applications. - : Springer Nature. - 2056-7189. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of upstream regulatory genes of a gene of interest still remains challenging. Here we applied a scalable computational method to unbiasedly predict candidate regulatory genes of critical transcription factors by searching the whole genome. We illustrated our approach with a case study on the master regulator FOXP3 of human primary regulatory T cells (Tregs). While target genes of FOXP3 have been identified, its upstream regulatory machinery still remains elusive. Our methodology selected five top-ranked candidates that were tested via proof-of-concept experiments. Following knockdown, three out of five candidates showed significant effects on the mRNA expression of FOXP3 across multiple donors. This provides insights into the regulatory mechanisms modulating FOXP3 transcriptional expression in Tregs. Overall, at the genome level this represents a high level of accuracy in predicting upstream regulatory genes of key genes of interest.
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| 8. |
- Ni, Xiangyin, et al.
(författare)
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Formation of forest gaps accelerates C, N and P release from foliar litter during 4 years of decomposition in an alpine forest
- 2018
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Ingår i: Biogeochemistry. - : Springer Science and Business Media LLC. - 0168-2563 .- 1573-515X. ; 139:3, s. 321-335
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Tidskriftsartikel (refereegranskat)abstract
- Relative to areas under canopy, the soils in forest gaps receive more irradiance and rainfall (snowfall); this change in microclimate induced by forest gaps may influence the release of carbon (C) and nutrients during litter decomposition. However, great uncertainty remains about the effects of forest gaps on litter decomposition. In this study, we incubated foliar litters from six tree and shrub species in forest gaps and canopy plots and measured the release of C, nitrogen (N) and phosphorus (P) in different snow cover periods in an alpine forest from 2012 to 2016. We found that N was retained by 24–46% but that P was immediately released during an early stage of decomposition. However, forest gaps decreased litter N retention, resulting in more N and P being released from decomposing litters for certain species (i.e., larch, birch and willow litters). Moreover, the release of C and nutrients during litter decomposition stimulated by forest gaps was primarily driven by warmer soil temperature in this high-altitude forest. We conclude that gap formation during forest regeneration may accelerate C turnover and nutrient cycling and that this stimulation might be regulated by the litter species in this seasonally snow-covered forest. © 2018, Springer Nature Switzerland AG.
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| 9. |
- Ni, Yuanzhi, et al.
(författare)
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Toward Reliable and Scalable Internet-of-Vehicles : Performance Analysis and Resource Management
- 2020
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Ingår i: Proceedings of the IEEE. - New York, NY : Institute of Electrical and Electronics Engineers (IEEE). - 0018-9219 .- 1558-2256. ; 108:2, s. 324-340
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Tidskriftsartikel (refereegranskat)abstract
- Reliable and scalable wireless transmissions for Internet-of-Vehicles (IoV) are technically challenging. Each vehicle, from driver-assisted to automated one, will generate a flood of information, up to thousands of times of that by a person. Vehicle density may change drastically over time and location. Emergency messages and real-time cooperative control messages have stringent delay constraints while infotainment applications may tolerate a certain degree of latency. On a congested road, thousands of vehicles need to exchange information badly, only to find that service is limited due to the scarcity of wireless spectrum. Considering the service requirements of heterogeneous IoV applications, service guarantee relies on an in-depth understanding of network performance and innovations in wireless resource management leveraging the mobility of vehicles, which are addressed in this article. For single-hop transmissions, we study and compare the performance of vehicle-to-vehicle (V2V) beacon broadcasting using random access-based (IEEE 802.11p) and resource allocation-based (cellular vehicle-to-everything) protocols, and the enhancement strategies using distributed congestion control. For messages propagated in IoV using multihop V2V relay transmissions, the fundamental network connectivity property of 1-D and 2-D roads is given. To have a message delivered farther away in a sparse, disconnected V2V network, vehicles can carry and forward the message, with the help of infrastructure if possible. The optimal locations to deploy different types of roadside infrastructures, including storage-only devices and roadside units with Internet connections, are analyzed. © 2019 IEEE
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