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result(s) for
"Shuai-peng, Yang"
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Adenine base-editing-mediated exon skipping induces gene knockout in cultured pig cells
2022
Gene-knockout pigs have important applications in agriculture and medicine. Compared with CRISPR/Cas9, Adenine base editor (ABE) convert single A·T pairs to G·C pairs in the genome without generating DNA double-strand breaks, and this method has higher accuracy and biosafety in pig genetic modification. However, the application of ABE in pig gene knockout is limited by protospacer-adjacent motif sequences and the base-editing window. Alternative mRNA splicing is an important mechanism underlying the formation of proteins with diverse functions in eukaryotes. Spliceosome recognizes the conservative sequences of splice donors and acceptors in a precursor mRNA. Mutations in these conservative sequences induce exon skipping, leading to proteins with novel functions or to gene inactivation due to frameshift mutations. In this study, adenine base-editing-mediated exon skipping was used to expand the application of ABE in the generation of gene knockout pigs. We first constructed a modified “all-in-one” ABE vector suitable for porcine somatic cell transfection that contained an ABE for single-base editing and an sgRNA expression cassette. The “all-in-one” ABE vector induced efficient sgRNA-dependent A-to-G conversions in porcine cells during single base-editing of multiple endogenous gene loci. Subsequently, an ABE system was designed for single adenine editing of the conservative splice acceptor site (AG sequence at the 3′ end of the intron 5) and splice donor site (GT sequence at the 5′ end of the intron 6) in the porcine gene GHR; this method achieved highly efficient A-to-G conversion at the cellular level. Then, porcine single-cell colonies carrying a biallelic A-to-G conversion in the splice acceptor site in the intron 5 of GHR were generated. RT-PCR indicated exon 6 skipped at the mRNA level. Western blotting revealed GHR protein loss, and gene sequencing showed no sgRNA-dependent off-target effects. These results demonstrate accurate adenine base-editing-mediated exon skipping and gene knockout in porcine cells. This is the first proof-of-concept study of adenine base-editing-mediated exon skipping for gene regulation in pigs, and this work provides a new strategy for accurate and safe genetic modification of pigs for agricultural and medical applications.
Journal Article
Production of MSTN knockout porcine cells using adenine base-editing-mediated exon skipping
by
Qu, Zi-xiao
,
Luo, Zi-dan
,
Yan, Ai-fen
in
Adenine
,
Alternative splicing
,
Animal Genetics and Genomics
2023
Gene-knockout pigs have important applications in agriculture and medicine. Compared with CRISPR/Cas9 and cytosine base editing (CBE) technologies, adenine base editing (ABE) shows better safety and accuracy in gene modification. However, because of the characteristics of gene sequences, the ABE system cannot be widely used in gene knockout. Alternative splicing of mRNA is an important biological mechanism in eukaryotes for the formation of proteins with different functional activities. The splicing apparatus recognizes conserved sequences of the 5′ end splice donor and 3′ end splice acceptor motifs of introns in pre-mRNA that can trigger exon skipping, leading to the production of new functional proteins, or causing gene inactivation through frameshift mutations. This study aimed to construct a
MSTN
knockout pig by inducing exon skipping with the aid of the ABE system to expand the application of the ABE system for the preparation of knockout pigs. In this study, first, we constructed ABEmaxAW and ABE8eV106W plasmid vectors and found that their editing efficiencies at the targets were at least sixfold and even 260-fold higher than that of ABEmaxAW by contrasting the editing efficiencies at the gene targets of endogenous
CD163
,
IGF2
, and
MSTN
in pigs. Subsequently, we used the ABE8eV106W system to realize adenine base (the base of the antisense strand is thymine) editing of the conserved splice donor sequence (5′-GT) of intron 2 of the porcine
MSTN
gene. A porcine single-cell clone carrying a homozygous mutation (5′-GC) in the conserved sequence (5′-GT) of the intron 2 splice donor of the
MSTN
gene was successfully generated after drug selection. Unfortunately, the
MSTN
gene was not expressed and, therefore, could not be characterized at this level. No detectable genomic off-target edits were identified by Sanger sequencing. In this study, we verified that the ABE8eV106W vector had higher editing efficiency and could expand the editing scope of ABE. Additionally, we successfully achieved the precise modification of the alternative splice acceptor of intron 2 of the porcine
MSTN
gene, which may provide a new strategy for gene knockout in pigs.
Journal Article
Phase Transformation and Its Effect on Mechanical Properties of C300 Weld Metal after Aging Treatment at Different Temperatures
2015
The influence of aging temperature on phase transformation and mechanical properties of weld metal of maraging steel (grade C300) was studied. Microstructure was analyzed by means of optical microscopy, transmission e leetron microscopy, scanning electron microscopy and energy dispersive spectrum analysis. Gibbs free energy of Nia Ti and Fez Mo at different temperature was calculated by Thermal-calc software. The microstructure of weld metal in as- welded state is martensite. The yield strength of weld metal after 430 ℃ aging process may increase to 1561 MPa from 890 MPa in as-welded state, which is ascribed to the formation of spinodal constitute and GP zones. After 480 ℃ aging process, there are great deal of NiaTi precipitates in the martensite matrix and 10% reverted austenite phase in the cellular grain boundary, and the yield strength increases to 1 801 MPa. After aging process at 580 ℃ , there are many Fe2 Mo precipitates in the martensite matrix and 30%o reverted austenite phase in the cellular grain boundary, and the yield strength is 1329 MPa, which ls the lowest among the three cases. The phase transformation may also influence the toughness. It is found that precipitates make the toughness decrease and reverted austenite increases it. The mechanism of phase transformation on strength and toughness is discussed.
Journal Article
Investigating the initiation and propagation processes of convection in heavy precipitation over the western Sichuan Basin
2017
Heavy precipitation events occur often over the western Sichuan Basin in summer, near the transition zone between the Sichuan Basin and the steep terrain of the Tibetan Plateau. One such event - a heavy precipitation process that occurred on 18-20 August 2010, with clear nocturnal peaks - is chosen as a case to tentatively explore how the convection associated with convective-scale precipitation is initiated and propagated. By utilizing the vertical momentum equation from the viewpoint of separating perturbation pressure into dynamic and thermal parts, it is demonstrated that the vertical momentum is induced by the imbalance of several forces, including the dynamic/buoyant part of the perturbation pressure gradient force and the buoyancy force, with the latter dominating during the nocturnal-peak period. Although a negative value of the dynamic perturbation pressure gradient force partly offsets the positive buoyant forcing inside the strong updraft, the pattern of vertical motion tendency is largely attributable to its buoyancy because of its larger magnitude. Relative to the buoyancy component, the dynamic part of the vertical perturbation pressure gradient is also examined, revealing a smaller order of magnitude. Thus, it is the thermal effect that should be responsible for the initiation and propagation of convection. As for the convective-scale precipitation, it always presents a trailing morphology relative to the strong leading-side updraft. Furthermore, overlapping strong signals of vertical motion and its tendency point towards strong precipitation in the future.
Journal Article
Single-cell transcriptomics unveils xylem cell development and evolution
by
Tung, Chia-Chun
,
Liou, Pin-Chien
,
Huang, Chia-En
in
Animal Genetics and Genomics
,
Bioinformatics
,
Biomedical and Life Sciences
2023
Background
Xylem, the most abundant tissue on Earth, is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells. In most angiosperms, fusiform cells comprise vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed by tracheids in other vascular plants such as gymnosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types.
Results
Through both single-cell and laser capture microdissection transcriptomic profiling, we determine the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Based on cross-species analyses of single-cell clusters and overlapping trajectories, we reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots
Populus trichocarpa
and
Eucalyptus grandis
share nearly identical fusiform lineages, whereas the more basal angiosperm
Liriodendron chinense
has a fusiform lineage distinct from that in core eudicots. The tracheids in the basal eudicot
Trochodendron aralioides
, an evolutionarily reversed trait, exhibit strong transcriptomic similarity to vessel elements rather than libriform fibers.
Conclusions
This evo-devo framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history.
Journal Article
Research Progress of Non-Noble Metal Catalysts for Carbon Dioxide Methanation
by
Xu, Lujing
,
Lin, Congji
,
Peng, Shuai
in
Air quality management
,
Alternative energy sources
,
Carbon dioxide
2024
The extensive utilization of fossil fuels has led to a rapid increase in atmospheric CO2 concentration, resulting in various environmental issues. To reduce reliance on fossil fuels and mitigate CO2 emissions, it is important to explore alternative methods of utilizing CO2 and H2 as raw materials to obtain high-value-added chemicals or fuels. One such method is CO2 methanation, which converts CO2 and H2 into methane (CH4), a valuable fuel and raw material for other chemicals. However, CO2 methanation faces challenges in terms of kinetics and thermodynamics. The reaction rate, CO2 conversion, and CH4 yield need to be improved to make the process more efficient. To overcome these challenges, the development of suitable catalysts is essential. Non-noble metal catalysts have gained significant attention due to their high catalytic activity and relatively low cost. In this paper, the thermodynamics and kinetics of the CO2 methanation reaction are discussed. The focus is primarily on reviewing Ni-based, Co-based, and other commonly used catalysts such as Fe-based. The effects of catalyst supports, preparation methods, and promoters on the catalytic performance of the methanation reaction are highlighted. Additionally, the paper summarizes the impact of reaction conditions such as temperature, pressure, space velocity, and H2/CO2 ratio on the catalyst performance. The mechanism of CO2 methanation is also summarized to provide a comprehensive understanding of the process. The objective of this paper is to deepen the understanding of non-noble metal catalysts in CO2 methanation reactions and provide insights for improving catalyst performance. By addressing the limitations of CO2 methanation and exploring the factors influencing catalyst effectiveness, researchers can develop more efficient and cost-effective catalysts for this reaction.
Journal Article
Study of Five-Hundred-Meter Aperture Spherical Telescope Feed Cabin Time-Series Prediction Studies Based on Long Short-Term Memory–Self-Attention
by
Li, Jiaxue
,
Peng, Shuai
,
Song, Benning
in
Accuracy
,
Archives & records
,
Artificial intelligence
2024
The Five-hundred-meter Aperture Spherical Telescope (FAST), as the world’s most sensitive single-dish radio telescope, necessitates highly accurate positioning of its feed cabin to utilize its full observational potential. Traditional positioning methods that rely on GNSS and IMU, integrated with TS devices, but the GNSS and TS devices are vulnerable to other signal and environmental disruptions, which can significantly diminish position accuracy and even cause observation to stop. To address these challenges, this study introduces a novel time-series prediction model that integrates Long Short-Term Memory (LSTM) networks with a Self-Attention mechanism. This model can hold the precision of feed cabin positioning when the measure devices fail. Experimental results show that our LSTM-Self-Attention model achieves a Mean Absolute Error (MAE) of less than 10 mm and a Root Mean Square Error (RMSE) of approximately 12 mm, with the errors across different axes following a near-normal distribution. This performance meets the FAST measurement precision requirement of 15 mm, a standard derived from engineering practices where measurement accuracy is set at one-third of the control accuracy, which is around 48 mm (according to the accuracy form the official threshold analysis on the focus cabin of FAST). This result not only compensates for the shortcomings of traditional methods in consistently solving feed cabin positioning, but also demonstrates the model’s ability to handle complex time-series data under specific conditions, such as sensor failures, thus providing a reliable tool for the stable operation of highly sensitive astronomical observations.
Journal Article
Semi-supervised 3D shape segmentation with multilevel consistency and part substitution
by
Yang, Yu-Qi
,
Tong, Xin
,
Sun, Chun-Yu
in
Artificial Intelligence
,
Computer Graphics
,
Computer Science
2023
The lack of fine-grained 3D shape segmentation data is the main obstacle to developing learning-based 3D segmentation techniques. We propose an effective semi-supervised method for learning 3D segmentations from a few labeled 3D shapes and a large amount of unlabeled 3D data. For the unlabeled data, we present a novel
multilevel consistency
loss to enforce consistency of network predictions between perturbed copies of a 3D shape at multiple levels: point level, part level, and hierarchical level. For the labeled data, we develop a simple yet effective part substitution scheme to augment the labeled 3D shapes with more structural variations to enhance training. Our method has been extensively validated on the task of 3D object semantic segmentation on PartNet and ShapeNetPart, and indoor scene semantic segmentation on ScanNet. It exhibits superior performance to existing semi-supervised and unsupervised pre-training 3D approaches.
Journal Article
Thermally conductive composite phase change materials with excellent thermal management capability for electronic devices
by
Wang, Shuai-Peng
,
Zeng, Xian-Qing
,
Shen-Tu, Hong-Qian
in
Characterization and Evaluation of Materials
,
Chemistry and Materials Science
,
Electronic devices
2022
With the innovation of electronics industry and the advancement in 5G technology, the overheating problem has become an urgent obstacle to further realize the high performance and multi-function of electronic devices. Thus, it is essential to develop efficient thermal management materials to realize timely and effective heat dissipation. The thermal management systems based on phase change materials (PCMs) have received extensive attention in recent years. In this work, composite PCMs with a high phase change enthalpy of 149.56 J g
−1
, multiple phase change characteristics, a high thermal conductivity of 1.28 Wm
−1
K
−1
, and excellent shape stability were fabricated by the means of cross-linked polymer swelling strategy. When the as-prepared composite PCMs were directly attached to the heating plate or served as thermal interface materials (TIMs) to dissipate heat, the temperature of heating plate can be reduced by 5.8 °C and 18.8 °C, respectively, revealing great potential in the thermal management application of electronic devices.
Journal Article