| 1. |
|
|
| 2. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 3. |
- Liu, Hui, et al.
(författare)
-
Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
|
|
| 4. |
- Tian, Shiwei, et al.
(författare)
-
Investigation on the microstructure evolution and dynamic recrystallization mechanisms of TiAl alloy at elevated temperature
- 2021
-
Ingår i: Journal of Materials Research and Technology. - : Elsevier BV. - 2238-7854. ; 14, s. 968-984
-
Tidskriftsartikel (refereegranskat)abstract
- The flow stress–strain curves appear to be sensitive to deformation conditions. The ratio of critical strain to peak strain εc/εp follows a linear relationship except when the temperature is 1240 °C and the strain rate is 0.001 s−1. During the deformation, the fragmentation and decomposition of γ/α2 lamellae are related to recrystallization of α2 and γ laths in the lamellae and the γ → α2 phase transformation, the former depends on dislocation slip and twinning, and the latter is related to temperature, local stress concentration and diffusion time. As for the recrystallization mechanisms, the γ phase is discontinuous dynamic recrystallization (DDRX) mode, while the α2 phase relies on continuous dynamic recrystallization (CDRX) mode. The β phase has more low-angle grain boundaries (LAGB) during deformation, indicating the continuous coordinated deformation, and this explains the enlarged hot working window of the TiAl alloy (1165–1240 °C/0.001 ~ 1 s−1 and 1120–1165 °C/0.001–0.4 s−1).
|
|
| 5. |
- Cheng, Shi-Ping, et al.
(författare)
-
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
-
Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
|
|
| 6. |
- Huang, Zi-Nan, et al.
(författare)
-
Analysis of the stress field in the reactor vessel of the China Initiative Accelerator Driven System during postulated ULOF and UTOP transients
- 2023
-
Ingår i: Annals of Nuclear Energy. - : Elsevier BV. - 0306-4549 .- 1873-2100. ; 194
-
Tidskriftsartikel (refereegranskat)abstract
- The China Initiative Accelerator Driven System (CiADS) was proposed by China Academy of Science since 2015. The subcritical reactor in CiADS is a liquid Lead Bismuth Eutectic (LBE) cooled fast reactor. When the reactor core is in operation, the LBE coolant will directly contact and corrode the inner surface of reactor vessel. Due to the high temperature, the corrosion will be more severe. If the stress on the reactor vessel exceeds the limit, the plastic deformation will occur, leading to the generation and expansion of defects and cracks, and the safety of the reactor will be affected. Therefore, evaluating the stress field of the reactor vessel under different operating conditions is a very important research project. In this paper, the finite element analysis software ADINA was applied to analyze the reactor vessel in CiADS, and the ASME Code was used as stress assessment standards. We can preliminarily prove that the stress assessments of the vessel during the postulated Unprotected Loss of Flow (ULOF) accidents satisfy the requirements of ASME Code. The limit reactivity insertion to protect the vessel from plastic deformation is 0.58$ in the postulated Unprotected Transient over Power (UTOP) accidents based on our current results. Therefore, we can preliminarily conclude that the current material selection and structural design of the reactor vessel in CiADS could survive most of the postulated transient accidents considering the stress effect.
|
|
| 7. |
- Shiwei, Tian, et al.
(författare)
-
Effect of Mo Element on Microstructure and Mechanical Properties of TiAl Alloys
- 2022
-
Ingår i: Xiyou jinshu cailiao yu gongcheng. - : NORTHWEST INST NONFERROUS METAL RESEARCH. - 1002-185X. ; 51:7, s. 2336-2343
-
Tidskriftsartikel (refereegranskat)abstract
- Four TiAl alloys with different Mo contents were designed, and the microstructure and mechanical properties of these MoTiAl alloys were studied by scanning electron microscope, nanoindentation, and hot compression simulation methods. Results show that with increasing the Mo content, the content of. phase is gradually decreased, while that of beta phase is gradually increased. The Mo element mainly exists in the form of beta phase in the TiAl alloy. During the hot isostatic pressing process, the Mo element is diffused from the. and a 2 phases to the beta phase. The nanoindentation hardness of Mo-TiAl alloy reaches the maximum when the Mo content is 1.59at%, and it is negatively correlated with the interlamellar space. As the content of Mo element increases, the flow stress of Mo-TiAl alloys decreases, and the TiAl alloys with 2.11at% and 3.94at% Mo addtion have poor plasticity due to the Al element segregation.
|
|
| 8. |
- Shiwei, Tian, et al.
(författare)
-
Oxidation resistance of TiAl alloy improved by hot-pack rolling and cyclic heat treatment
- 2021
-
Ingår i: Materials Characterization. - : Elsevier BV. - 1044-5803 .- 1873-4189. ; 178
-
Tidskriftsartikel (refereegranskat)abstract
- The isothermal oxidation behavior of two TiAl alloys (as-HIP and as-RHT) were compared to explain the effect of microstructure on the oxidation resistance of TiAl alloy. After hot-pack rolling and cyclic heat treatment, the size of lamellar colonies was refined from 35.4 mu m to 21.5 mu m, and the beta/B2 phase was effectively removed. It is concluded that the as-RHT TiAl alloy has better oxidation resistance than the as-HIP TiAl alloy. The main reason is due to refinement of lamellar colony size, elimination of beta/B2 phase, uniform distribution of Nb and Mo, and the crushing of Y compounds.
|
|
| 9. |
- Yang, Fu-Sheng, et al.
(författare)
-
Chromosome-level genome assembly of a parent species of widely cultivated azaleas
- 2020
-
Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing to the genomic architecture of flowering time. Small-scale gene duplications contribute to the expansion of gene families involved in azalea pigment biosynthesis. We reconstruct entire metabolic pathways for anthocyanins and carotenoids and their potential regulatory networks by detailed analysis of time-ordered gene co-expression networks. MYB, bHLH, and WD40 transcription factors may collectively regulate anthocyanin accumulation in R. simsii, particularly at the initial stages of flower coloration, and with WRKY transcription factors controlling progressive flower coloring at later stages. This work provides a cornerstone for understanding the underlying genetics governing flower timing and coloration and could accelerate selective breeding in azalea. Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.
|
|
| 10. |
- Yang, Shun, et al.
(författare)
-
Reversibly modulating a conformation-adaptive fluorophore in [2]catenane
- 2021
-
Ingår i: Chem. - : Elsevier BV. - 2451-9308 .- 2451-9294. ; 7:6, s. 1544-1556
-
Tidskriftsartikel (refereegranskat)abstract
- Tuning molecular emission by chemicalmeans has long been a fundamental topic, because the emerging methodologies and mechanisms of this topic usually bring a lot of opportunities in many multi-disciplinary applications. Here, we demonstrate the reversible switching of a conformation-adaptive fluorophore, 9,14-diphenyl-9,14-dihydrodibenzo[ a,c]phenazine (DPAC), by incorporating this fluorescent unit into a mechanically interlocked [2]catenane. Taking advantage of the mechanical bond of [2]catenane, the conformational freedom of the DPAC-macrocycle can be modulated by the co-conformational state of the [2]catenane, thus enabling the reversible switching of the fluorescent properties of DPAC. Owing to the mechanically interlocked structure, this fluorescent molecular system can be switched in a dual-mode (wavelength or intensity), visually recognizable, and highly reversible manner. This work provides a distinctmechanism of switchingmolecular emission by modulating conformation-adaptive fluorescent systems in mechanically interlocked structures.
|
|
