| 1. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 2. |
- Wang, Longxin, et al.
(författare)
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Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Quercus variabilis)
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The Quercus variabilis, a deciduous broadleaved tree species, holds significant ecological and economical value. While a chromosome-level genome for this species has been made available, it remains riddled with unanchored sequences and gaps. In this study, we present a nearly complete comprehensive telomere-to-telomere (T2T) and haplotype-resolved reference genome for Q. variabilis. This was achieved through the integration of ONT ultra-long reads, PacBio HiFi long reads, and Hi-C data. The resultant two haplotype genomes measure 789 Mb and 768 Mb in length, with a contig N50 of 65 Mb and 56 Mb, and were anchored to 12 allelic chromosomes. Within this T2T haplotype-resolved assembly, we predicted 36,830 and 36,370 protein-coding genes, with 95.9% and 96.0% functional annotation for each haplotype genome. The availability of the T2T and haplotype-resolved reference genome lays a solid foundation, not only for illustrating genome structure and functional genomics studies but also to inform and facilitate genetic breeding and improvement of cultivated Quercus species.
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| 3. |
- Li, Suyang, et al.
(författare)
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Highly homogeneous bimetallic core-shell Au@Ag nanoparticles with embedded internal standard fabrication using a microreactor for reliable quantitative SERS detection
- 2023
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Ingår i: Materials Chemistry Frontiers. - : Royal Society of Chemistry (RSC). - 2052-1537. ; 7:6, s. 1100-1109
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Tidskriftsartikel (refereegranskat)abstract
- Bimetallic gold core-silver shell (Au@Ag) surface-enhanced Raman scattering tags draw broad interest in the fields of biological and environmental analyses. Herein, an efficient hybrid microfluidic chip was designed to prepare uniform Au@Ag core-shell nanoparticles, and DTNB was used as the internal standard tag molecule to prepare Au@DTNB@Ag for SERS detection. Homogeneous core-shell nanoparticles with a particle size of 90 nm were prepared by mixing a silver precursor and a gold core in a microfluidic chip. The relative standard deviation (RSD) of the particle size distribution was close to 10%, and the detection limit of 4-MBA was as low as 10-10 M. In order to solve the influence of SERS signal fluctuation, a uniform Au@DTNB@Ag core-molecule-shell structure was synthesized in a microfluidic chip, and the characteristic peak of the analyte was corrected by the relative intensity of the DTNB characteristic peak (1335 cm−1). The experimental results showed that the SERS detection was achieved with high reproducibility, and the SERS peak intensity had a good linear correlation with the concentration. The homogeneous SERS substrate prepared using a microfluidic chip has potential for sensitive and reliable detection of environmental chemical contaminants.
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| 4. |
- Yuan-Biao, Qiao, et al.
(författare)
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Antifungal resistance-modifying multiplexing action of Momordica charantia protein and phosphorylated derivatives on the basis of growth-dependent gene coregulation in Candida albicans
- 2021
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Ingår i: Medical Mycology. - : Oxford University Press. - 1369-3786 .- 1460-2709. ; 59:6, s. 515-527
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Tidskriftsartikel (refereegranskat)abstract
- Fungal growth-dependent gene coregulation is strongly implicated in alteration of gene-encoding target proteases ruling with an antifungal resistance niche and biology of resistant mutants. On the basis of multialterative processes in this platform, the resistance-modifying strategy is designed in ketoconazole resistant Candida albicans and evaluated with less selective Momordica charantia protein and allosterically phosphorylated derivatives at the Thr102, Thr24 and Thr255 sites, respectively. We demonstrate absolutely chemosensitizing efficacy regarding stepwise-modifying resistance in sensitivity, by a load of only 26.23-40.00 mu g/l agents in Sabouraud's dextrose broth. Five successive modifying-steps realize the decreasing of ketoconazole E-test MIC50 from 11.10 to a lower level than 0.10 mg/l. With the ketoconazole resistance-modifying, colony undergoes a high-frequency morphological switch between high ploidy (opaque) and small budding haploid (white). A cellular event in the first modifying-step associates with relatively slow exponential growth (ie, a 4-h delay)-dependent action, mediated by agents adsorption. Moreover, multiple molecular roles are coupled with intracellularly and extracellularly binding to ATP-dependent RNA helicase dbp6; the 0.08-2.45 fold upregulation of TATA-box-binding protein, rRNA-processing protein and translation initiation factor 5A; and the 7.52-55.33% decrease of cytochrome P450 lanosterol 14 alpha-demethylase, glucan 1, 3-beta glucosidase, candidapepsin-1 and 1-acylglycerol-3-phosphate O-acyltransferase. Spatial and temporal gene coregulation, in the transcription and translation initiation stages with rRNA-processing, is a new coprocessing platform enabling target protease attenuations for resistance-impairing. An updated resistance-modifying measure of these agents in the low-dose antifungal strategic design may provide opportunities to a virtually safe therapy that is in high dose-dependency.
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| 5. |
- Chen, Jie, 1974-, et al.
(författare)
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Revisiting Late Pleistocene Loess–Paleosol Sequences in the Azov Sea Region of Russia : Chronostratigraphy and Paleoenvironmental Record
- 2022
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Ingår i: Frontiers in Earth Science. - : Frontiers Media S.A.. - 2296-6463. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Loess-paleosol sequences are the most intensively studied terrestrial archives used for the reconstruction of Late Pleistocene environmental and climatic changes in the Azov Sea region, southwest Russia. Here we present a refined chronostratigraphy and a multiproxy record of Late Pleistocene environmental dynamics of the most complete and representative loess–paleosol sequences (Beglitsa and Chumbur-Kosa sections) from the Azov Sea region. We propose a new chronostratigraphy following the Chinese and Danubean loess stratigraphic models that refines the subdivision of the Last Interglacial paleosol (S1) complex in two Azov Sea sites, resolve the uncertainty of the stratigraphic position of the weakly developed paleosol (L1SSm) in Beglitsa section, and allow for direct correlation of the Azov Sea sections with those in the Danube Basin and the Chinese Loess Plateau. More importantly, it may serve as a basis for better constraining local and regional chronostratigraphic correlations, and facilitate the interpretation of climatic connections and possible forcing mechanisms responsible for the climatic trends in the region. In addition, a general succession of environmental dynamics is reconstructed from these two vital sections, which is broadly consistent with other loess records in the Dnieper Lowland and Lower Danube Basin, demonstrating similar climatic trends at Glacial–Interglacial time scales. Furthermore, our results have important implications for the chronostratigraphic representativeness of Beglitsa as a key regional loess section and for the reconstruction of the temporal and spatial evolution of Late Pleistocene climate in the Azov Sea region.
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| 6. |
- Chen, Yicheng, et al.
(författare)
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Computational fluid-structure interaction analysis of flapping uvula on aerodynamics and pharyngeal vibration in a pediatric airway
- 2023
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 13:1, s. 2013-
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Tidskriftsartikel (refereegranskat)abstract
- The uvula flapping is one of the most distinctive features of snoring and is critical in affecting airway aerodynamics and vibrations. This study aimed to elucidate the mechanism of pharyngeal vibration and pressure fluctuation due to uvula flapping employing fluid-structure interaction simulations. The followings are the methodology part: we constructed an anatomically accurate pediatric pharynx model and put attention on the oropharynx region where the greatest level of upper airway compliance was reported to occur. The uvula was assumed to be a rigid body with specific flapping frequencies to guarantee proper boundary conditions with as little complexity as possible. The airway tissue was considered to have a uniform thickness. It was found that the flapping frequency had a more significant effect on the airway vibration than the flapping amplitude, as the flapping uvula influenced the pharyngeal aerodynamics by altering the jet flow from the mouth. Breathing only through the mouth could amplify the effect of flapping uvula on aerodynamic changes and result in more significant oropharynx vibration.
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| 7. |
- Chen, Yicheng, et al.
(författare)
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Evaluation of computational fluid dynamics models for predicting pediatric upper airway airflow characteristics
- 2023
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Ingår i: Medical and Biological Engineering and Computing. - : Springer. - 0140-0118 .- 1741-0444. ; 61:1, s. 259-270
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Tidskriftsartikel (refereegranskat)abstract
- Computational fluid dynamics (CFD) has the potential for use as a clinical tool to predict the aerodynamics and respiratory function in the upper airway (UA) of children; however, careful selection of validated computational models is necessary. This study constructed a 3D model of the pediatric UA based on cone beam computed tomography (CBCT) imaging. The pediatric UA was 3D printed for pressure and velocity experiments, which were used as reference standards to validate the CFD simulation models. Static wall pressure and velocity distribution inside of the UA under inhale airflow rates from 0 to 266.67 mL/s were studied by CFD simulations based on the large eddy simulation (LES) model and four Reynolds-averaged Navier-Stokes (RANS) models. Our results showed that the LES performed best for pressure prediction; however, it was much more time-consuming than the four RANS models. Among the RANS models, the Low Reynolds number (LRN) SST k-ω model had the best overall performance at a series of airflow rates. Central flow velocity determined by particle image velocimetry was 3.617 m/s, while velocities predicted by the LES, LRN SST k-ω, and k-ω models were 3.681, 3.532, and 3.439 m/s, respectively. All models predicted jet flow in the oropharynx. These results suggest that the above CFD models have acceptable accuracy for predicting pediatric UA aerodynamics and that the LRN SST k-ω model has the most potential for clinical application in pediatric respiratory studies.
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| 8. |
- Chen, Yicheng, et al.
(författare)
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Impact of sleep posture and breathing pattern on soft palate flutter and pharynx vibration in a pediatric airway using fluid-structure interaction
- 2023
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Ingår i: Journal of Biomechanics. - : Elsevier. - 0021-9290 .- 1873-2380. ; 152
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Tidskriftsartikel (refereegranskat)abstract
- Snoring is a common condition in the general population, and the management of snoring requires a better understanding of its mechanism through a fluid-structure interaction (FSI) perspective. Despite the recent popularity of numerical FSI techniques, outstanding challenges are accurately predicting airway deformation and its vibration during snoring due to complex airway morphology. In addition, there still needs to be more un-derstanding of snoring inhibition when lying on the side, and the possible effect of airflow rates, as well as nose or mouth-nose breathing, on snoring remains to be investigated. In this study, an FSI method verified against in vitro models was introduced to predict upper airway deformation and vibration. The technique was applied to predict airway aerodynamics, soft palate flutter, and airway vibration in four sleep postures (supine, left/right lying, and sitting positions) and four breathing patterns (mouth-nose, nose, mouth, and unilateral nose breathing). It was found that, at given elastic properties of soft tissues, the evaluated flutter frequency of 19.8 Hz in inspiration was in good agreement with the reported frequency of snoring sound in literature. Reduction in flutter and vibrations due to the mouth-nose airflow proportion changes were also noticed when having side-lying and sitting positions. Breathing through the mouth results in larger airway deformation than breathing through the nose or mouth-nose. These results collectively demonstrate the potential of FSI for studying the physics of airway vibration and clarify to some degree the reason for snoring inhibition during sleep postures and breathing patterns.
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| 9. |
- Chen, Yifeng, et al.
(författare)
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Kinetics study and performance comparison of CO2 separation using aqueous choline-amino acid solutions
- 2021
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Ingår i: Separation and Purification Technology. - : Elsevier. - 1383-5866 .- 1873-3794. ; 261
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Tidskriftsartikel (refereegranskat)abstract
- The thermodynamic and kinetic properties of CO2 in aqueous choline-amino acids ([Cho][AA]s) are important information to demonstrate their performance. In this study, the apparent kinetic properties of CO2 in the five aqueous [Cho][AA]s, including the liquid-side mass-transfer coefficients, enhancement factor, and reaction rate constant, were systematically studied. Furthermore, a new ‘‘absorption ability’’ (AA) index was proposed, combining the apparent kinetic properties determined in this study and thermodynamic properties determined in our previous study. The CO2 separation performance using aqueous [Cho][AA]s was evaluated based on the AA and CO2 desorption enthalpy values. The results show that 30 wt% aqueous choline-serine is a promising absorbent for CO2 separation, and it is comparable to aqueous monoethanolamine.
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| 10. |
- Li, Suyang, et al.
(författare)
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One-pot fabrication of Mo1-xWxS2 alloy nanosheets as SERS substrates with highly Raman enhancement effect and long-term stability
- 2022
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Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : Elsevier BV. - 1386-1425 .- 1873-3557. ; 279, s. 121465-
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Tidskriftsartikel (refereegranskat)abstract
- A new Mo1-xWxS2 two-dimensional nanosheets were prepared by the one-pot method. After certain Mo atoms in MoS2 were replaced by W ones in a hydrothermal reduction procedure, Mo1-xWxS2 was formed on the Mo foil. Well enhanced Mo1-xWxS2 nanosheets were prepared when the sodium tungstate concentration got under control. Various characterizations were carried out, which indicate that Mo1-xWxS2 nanosheets with good crystallinity. Compared with MoS2, the Raman intensity of Rhodamine 6G (10-6 M) was amplified by 1.7 times with Mo1-xWxS2 nanosheets as the substrate. The characteristic Raman peaks could still be clearly distinguished until the concentration of Rhodamine 6G (R6G), Methylene blue (MB) and Crystal violet (CV) down to 10-8, 10-8 and 10- 7 M, respectively. With abundant edge active sites that facilitate charge transfer, Mo1-xWxS2 nanosheets could better enhance SERS signals of target detection molecules and get a good linear relationship exists within the concentration and Raman peak strength. In addition, R6G SERS detection also shows excellent reproducibility and long-term stability of this TMDs SERS substrate.
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