| 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. |
- Liu, Shuyu, et al.
(författare)
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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome
- 2022
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:2
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.
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| 3. |
- Shi, Tingting, et al.
(författare)
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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees
- 2024
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Ingår i: Molecular Plant. - : Elsevier. - 1674-2052 .- 1752-9867. ; 17:5, s. 725-746
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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| 4. |
- Chen, Zemeng, et al.
(författare)
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Open access dataset integrating EEG and fNIRS during Stroop tasks
- 2023
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Conflict monitoring and processing are crucial components of the human cognitive system, with significant implications for daily life and the diagnosis of cognitive disorders. The Stroop task, combined with brain function detection technology, has been widely employed as a classical paradigm for investigating conflict processing. However, there remains a lack of public datasets that integrate Electroencephalogram (EEG) and functional Near-infrared Spectroscopy (fNIRS) to simultaneously record brain activity during a Stroop task. We introduce a dual-modality Stroop task dataset incorporating 34-channel EEG (sampling frequency is 1000 Hz) and 20-channel high temporal resolution fNIRS (sampling frequency is 100 Hz) measurements covering the whole frontal cerebral cortex from 21 participants (9 females/12 males, aged 23.0 ± 2.3 years). Event-related potential analysis of EEG recordings and activation analysis of fNIRS recordings were performed to show the significant Stroop effect. We expected that the data provided would be utilized to investigate multimodal data processing algorithms during cognitive processing.
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| 5. |
- Fan, Zhouzhou, et al.
(författare)
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Changes in Plant Rhizosphere Microbial Communities under Different Vegetation Restoration Patterns in Karst and Non-karst Ecosystems
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how patterns of recovery and geological conditions affect microbial communities is important for determining the stability of karst ecosystems. Here, we investigated the diversity and composition of microorganisms in karst and non-karst environments under natural restoration and artificial rehabilitation conditions. The results showed no significant differences in soil microbial diversity, but the microbial communities associated with geological conditions and tree species differed significantly. Variation partitioning analysis (VPA) showed that a total of 77.3% of the variation in bacteria and a total of 69.3% of the variation in fungi could be explained by vegetation type and geological background. There were significant differences in six bacterial classes (Actinobacteria, Alphaproteobacteria, Ktedonobacteria, TK10, Gammaproteobacteria, and Anaerolineae) and nine fungal classes (Eurotiomycetes, Agaricomycetes, unclassified _p_Ascomycota, Sordariomycetes, Tremellomycetes, norank_k_Fungi, Pezizomycetes, Leotiomycetes and Archaeorhizomycetes) among the soils collected from six plots. A Spearman correlation heatmap showed that the microbial community was affected by the major soil properties. Principal coordinates analysis indicated that the microbial community of Pinus yunnanensis in the artificial forest, which was established for the protection of the environment was most similar to that in the natural secondary forest in the karst ecosystem. These findings further our understanding of microbial responses to vegetation restoration and geological conditions.
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| 6. |
- Glicksberg, Benjamin S., et al.
(författare)
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Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits
- 2019
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Ingår i: BMC Medical Genomics. - : BMC. - 1755-8794. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundGenetic loss-of-function variants (LoFs) associated with disease traits are increasingly recognized as critical evidence for the selection of therapeutic targets. We integrated the analysis of genetic and clinical data from 10,511 individuals in the Mount Sinai BioMe Biobank to identify genes with loss-of-function variants (LoFs) significantly associated with cardiovascular disease (CVD) traits, and used RNA-sequence data of seven metabolic and vascular tissues isolated from 600 CVD patients in the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) study for validation. We also carried out in vitro functional studies of several candidate genes, and in vivo studies of one gene.ResultsWe identified LoFs in 433 genes significantly associated with at least one of 10 major CVD traits. Next, we used RNA-sequence data from the STARNET study to validate 115 of the 433 LoF harboring-genes in that their expression levels were concordantly associated with corresponding CVD traits. Together with the documented hepatic lipid-lowering gene, APOC3, the expression levels of six additional liver LoF-genes were positively associated with levels of plasma lipids in STARNET. Candidate LoF-genes were subjected to gene silencing in HepG2 cells with marked overall effects on cellular LDLR, levels of triglycerides and on secreted APOB100 and PCSK9. In addition, we identified novel LoFs in DGAT2 associated with lower plasma cholesterol and glucose levels in BioMe that were also confirmed in STARNET, and showed a selective DGAT2-inhibitor in C57BL/6 mice not only significantly lowered fasting glucose levels but also affected body weight.ConclusionIn sum, by integrating genetic and electronic medical record data, and leveraging one of the world's largest human RNA-sequence datasets (STARNET), we identified known and novel CVD-trait related genes that may serve as targets for CVD therapeutics and as such merit further investigation.
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| 7. |
- Gong, Guoqing, et al.
(författare)
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Anomalous Water Vapor Circulation in an Extreme Drought Event of the Mid-Reaches of the Lancang-Mekong River Basin
- 2024
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Ingår i: EARTHS FUTURE. - 2328-4277. ; 12:8
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Tidskriftsartikel (refereegranskat)abstract
- The middle reaches of the Lancang-Mekong River Basin (M-LMRB) experienced a record-breaking drought event in 2019, resulting in significant economic losses of approximately 650 million dollars and affecting a population of 17 million. However, the anomalous circulation and transportation processes of water vapor, which may have played a crucial role in inducing the extreme drought, have not been fully studied. In this study, we analyze the water vapor circulation during the 2019 drought event using the land-atmosphere water balance and a backward trajectory model for moisture tracking. Our results indicate that the precipitation in the M-LMRB from May to October 2019 was only 71.9% of the long-term climatological mean (1959-2021). The low precipitation during this drought event can be attributed to less-than-normal external water vapor supply. Specifically, the backward trajectory model reveals a decrease in the amount of water vapor transported from the Indian Ocean, the Bay of Bengal, and the Pacific Ocean, which are the main moisture sources for precipitation in the region. Comparing the atmospheric circulation patterns in 2019 with the climatology, we identify anomalous anticyclone conditions in the Bay of Bengal, anomalous westerlies in the Northeast Indian Ocean, and an anomalous cyclone in the Western Pacific Ocean, collectively facilitating a stronger export of water vapor from the region. Therefore, the dynamic processes played a more significant role than thermodynamic processes in contributing to the 2019 extreme drought event. In 2019, a record-breaking drought hit the M-LMRB, leading to significant economic losses and affecting a large population. This study explores the water vapor circulation during this drought using land-atmosphere water balance and a backward trajectory model. Findings show that precipitation from May to October 2019 was only seventy percent of the average from 1959 to 2021. The drought's severity was mainly due to a lack of water vapor from key sources: the Indian Ocean, the Bay of Bengal, and the Pacific Ocean. Anomalous weather patterns-an anticyclone in the Bay of Bengal, unusual westerlies in the Northeast Indian Ocean, and a cyclone in the Western Pacific-led to a significant reduction in water vapor reaching the region. This indicates that dynamic atmospheric processes played a larger role in causing the extreme drought than thermodynamic ones. These insights help improve understanding and prediction of droughts in Southeast Asia, particularly under changing climate conditions. Reduced external water vapor transport primarily leads to negative precipitation anomalies There has been a reduction in water vapor originating from the Indian Ocean, Bay of Bengal, and Pacific Ocean The reduction in water vapor transport is primarily influenced by dynamic factors rather than thermodynamic ones
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| 8. |
- Liu, Rongying, 1983-, et al.
(författare)
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Chirality Transfer of Glycopeptide across Scales Defined by the Continuity of Hydrogen Bonds
- 2024
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Ingår i: ACS Nano. - 1936-0851 .- 1936-086X. ; 18:22, s. 14367-14376
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Tidskriftsartikel (refereegranskat)abstract
- In nature, chirality transfer refines biomolecules across all size scales, bestowing them with a myriad of sophisticated functions. Despite recent advances in replicating chirality transfer with biotic or abiotic building blocks, a molecular understanding of the underlying mechanism of chirality transfer remains a daunting challenge. In this paper, the coassembly of two types of glycopeptide molecules differing in capability of forming intermolecular hydrogen bonds enabled the involvement of discontinuous hydrogen bond, which allowed for a nanoscale chirality transfer from glycopeptide molecules to chiral micelles, yet inhibited the micrometer scale chirality transfer toward helix formation, leading to an achiral transfer from chiral micelles to planar monolayer. Upon stacking the monolayer into a bilayer, the nonsuperimposable front and back faces of the chiral micelles involved in the monolayer ribbons lead to the opposite rotation of two layers toward increasing the continuity of H-bonds. The resultant continuity triggered the symmetry breaking of stacked bilayers and thus reactivated the micrometer-scale chirality transfer toward the final helix. This work delineates a promising step toward a better understanding and replicating the naturally occurring chirality transfer events and will be instructive to future chiral material design.
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| 9. |
- Ma, Mengnan, et al.
(författare)
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Summer regional climate simulations over Tibetan Plateau: from gray zone to convection permitting scale
- 2022
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Ingår i: Climate Dynamics. - : Springer Science and Business Media LLC. - 0930-7575 .- 1432-0894.
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Tidskriftsartikel (refereegranskat)abstract
- The Tibetan Plateau (TP) is often referred to as ‘the Third Pole’ and plays an essential role in the global climate. However, it remains challenging for most global and regional models to realistically simulate the characteristics of climate over the TP. In this study, two Weather Research and Forecasting model (WRF) experiments using spectral nudging with gray-zone (GZ9) and convection-permitting (CP3) resolution are conducted for summers from 2009 to 2018. The surface air temperature (T2m) and precipitation from the two simulations and the global reanalysis ERA5 are evaluated against in-situ observations. The results show that ERA5 has a general cold bias over southern TP, especially in maximum T2m (Tmax), and wet bias over whole TP. Both experiments can successfully capture the spatial pattern and daily variation of T2m and precipitation, though cold bias for temperature and dry bias for precipitation exist especially over the regions south of 35° N. Compared with ERA5, the added value of the two WRF experiments is mainly reflected in the reduced cold bias especially for Tmax with more improvement found in CP3 and the reduced wet bias. However, the ability of the convection-permitting WRF experiment in improving the simulation of precipitation seems limited when compared to the gray-zone WRF experiment, which may be related to the biases in physical parameterization and lack of representativeness of station observation. Further investigation into surface radiation budget reveals that the underestimation of net shortwave radiation contributes a lot to the cold bias of T2m over the southeastern TP in GZ9 which is improved in CP3. Compared with GZ9, CP3 shows that larger specific humidity at low-level (mid-high level) coexists with more precipitation (clouds) over the southern TP. This improvement is achieved by better depiction of topographic details, underlying surface and atmospheric processes, land–atmosphere interactions and so on, leading to stronger northward water vapor transport (WVT) in CP3, providing more water vapor for precipitation at surface and much wetter condition in the mid-high level.
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| 10. |
- Zhang, Shuyu, et al.
(författare)
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Moisture Sources and Pathways of Annual Maximum Precipitation in the Lancang-Mekong River Basin
- 2024
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Ingår i: GEOPHYSICAL RESEARCH LETTERS. - 0094-8276 .- 1944-8007. ; 51:6
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Tidskriftsartikel (refereegranskat)abstract
- Recent extremely heavy precipitation has led to substantial economic losses and affected millions of residences in the Lancang-Mekong River Basin (LMRB). This study analyzed the spatial-temporal characteristics of the annual maximum precipitation (R1X) of the LMRB and identified the moisture sources and pathways conducive to R1Xs using a Lagrangian back trajectory model. Results show that India Ocean and Bay of Bengal (IO/BOB), local evapotranspiration, and West Pacific Ocean and East China (WP/EC) are the three main moisture transport pathways of the R1Xs in LMRB, contributing 68.3%, 20.4% and 11.3% of the trajectories, respectively. R1Xs in the downstream eastern area are affected by tropical cyclones bringing large amounts of moisture from the WP/EC. As tropical cyclones shifted northward under climate change impact, more extreme precipitation occurred over the LMRB due to moisture coming from WP/EC, but those from the IO/BOB had decreased because of the slowdown of flows across the Equator. Recent extremely heavy precipitation has led to more frequent floods, storm surges, and other natural hazards in the Lancang-Mekong River Basin, resulting in substantial economic losses and affecting millions of residences. This study used annual maximum precipitation to represent the extreme precipitation and analyzed its spatial-temporal characteristics and the moisture sources and pathways. Results show that the extreme precipitation of the upstream region mainly occurred in July, while that of the downstream region mainly occurred in August-September. The moisture pathways of the historical extreme precipitation were identified using a physical-based model, and are classified into three clusters using a machine-learning model. West Pacific Ocean and East China, local evapotranspiration, and Indian Ocean and Bay of Bengal (IO/BOB) are the three moisture transport pathways with contributions of 68.3%, 20.4%, and 11.3% to the total pathways. The tropical cyclones bring large amounts of moisture and mainly affect R1Xs in the downstream eastern area. Tropical cyclones shifted northward under climate change impact, and more extreme precipitation occurred over the LMRB due to moisture coming from the West Pacific Ocean and East China, but those from the IO and BOB had decreased because of the slowdown of flows across the Equator. The timing of the annual maximum precipitation of the Lancang-Mekong River Basin (LMRB) varies from July to September The extreme precipitation of the LMRB mainly received moisture from the Indian Ocean to the West Pacific Ocean Tropical cyclones will bring more extreme precipitation to the LMRB under climate change
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