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"Zhang, Jia-Lin"
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Screening for functional circular RNAs using the CRISPR–Cas13 system
2021
Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood owing to the lack of adequate methods for distinguishing circRNAs from cognate messenger RNAs with overlapping exons. Here, we report that CRISPR–RfxCas13d can effectively discriminate circRNAs from mRNAs by using guide RNAs targeting sequences spanning back-splicing junction (BSJ) sites featured in RNA circles. Using a lentiviral library that targets sequences across BSJ sites of highly expressed human circRNAs, we show that a group of circRNAs are important for cell growth mostly in a cell-type-specific manner and that a common oncogenic circRNA, circFAM120A, promotes cell proliferation by preventing the mRNA for family with sequence similarity 120A (FAM120A) from binding the translation inhibitor IGF2BP2. Further application of RfxCas13d–BSJ-gRNA screening has uncovered circMan1a2, which has regulatory potential in mouse embryo preimplantation development. Together, these results establish CRISPR–RfxCas13d as a useful tool for the discovery and functional study of circRNAs at both individual and large-scale levels.This paper describes a CRISPR–Cas13 system to effectively target circRNAs and screen their functions in vitro and in vivo, which enables the study of relevant circRNA phenotypes in human cell proliferation and in mouse embryogenesis.
Journal Article
Electrostatic Self-Assembly of CdS Quantum Dots with Co9S8 Hollow Nanotubes for Enhanced Visible Light Photocatalytic H2 Production
2024
CdS quantum dots (CdS QDs) are regarded as a promising photocatalyst due to their remarkable response to visible light and suitable placement of conduction bands and valence bands. However, the problem of photocorrosion severely restricts their application. Herein, the CdS QDs-Co9S8 hollow nanotube composite photocatalyst has been successfully prepared by loading Co9S8 nanotubes onto CdS QDs through an electrostatic self-assembly method. The experimental results show that the introduction of Co9S8 cocatalyst can form a stable structure with CdS QDs, and can effectively avoid the photocorrosion of CdS QDs. Compared with blank CdS QDs, the CdS QDs-Co9S8 composite exhibits obviously better photocatalytic hydrogen evolution performance. In particular, CdS QDs loaded with 30% Co9S8 (CdS QDs-30%Co9S8) demonstrate the best photocatalytic performance, and the H2 production rate reaches 9642.7 μmol·g−1·h−1, which is 60.3 times that of the blank CdS QDs. A series of characterizations confirm that the growth of CdS QDs on Co9S8 nanotubes effectively facilitates the separation and migration of photogenerated carriers, thereby improving the photocatalytic hydrogen production properties of the composite. We expect that this work will facilitate the rational design of CdS-based photocatalysts, thereby enabling the development of more low-cost, high-efficiency and high-stability composites for photocatalysis.
Journal Article
Recent Developments and Perspectives of Cobalt Sulfide-Based Composite Materials in Photocatalysis
2023
Photocatalysis, as an inexpensive and safe technology to convert solar energy, is essential for the efficient utilization of sustainable renewable energy sources. Earth-abundant cobalt sulfide-based composites have generated great interest in the field of solar fuel conversion because of their cheap, diverse structures and facile preparation. Over the past 10 years, the number of reports on cobalt sulfide-based photocatalysts has increased year by year, and more than 500 publications on the application of cobalt sulfide groups in photocatalysis can be found in the last three years. In this review, we initially summarize the four common strategies for preparing cobalt sulfide-based composite materials. Then, the multiple roles of cobalt sulfide-based cocatalysts in photocatalysis have been discussed. After that, we present the latest progress of cobalt sulfide in four fields of photocatalysis application, including photocatalytic hydrogen production, carbon dioxide reduction, nitrogen fixation, and photocatalytic degradation of pollutants. Finally, the development prospects and challenges of cobalt sulfide-based photocatalysts are discussed. This review is expected to provide useful reference for the construction of high-performance cobalt sulfide-based composite photocatalytic materials for sustainable solar-chemical energy conversion.
Journal Article
Robust Schur complement preconditioner for block-Toeplitz system and its application in image restoration
2023
In this paper, we are mainly concerned with the iterative method for solving the block-Toeplitz linear system. Based on the exact block Schur complement factorization of the block-Toeplitz coefficient matrix, a class of parameterized robust Schur complement preconditioner is constructed, which relies on Sherman-Morrison-Woodbury inversion formula of the Schur complement of the partitioned coefficient matrix. Meanwhile, we show that the new preconditioned system can result in much better spectrum distributions than some existing preconditioners, and deflate some small eigenvalues of the preconditioned matrix. The convergence analysis of our proposed method is established, and a strategy for the practical choice of an optimal parameter is given. Numerical experiments arising from image restoration are provided, which show the proposed preconditioner is effective and confirm our theoretical results are correct.
Journal Article
Controlled Fabrication of Uniform Digital Nanorods from Precise Sequence-Defined Amphiphilic Polymers in Aqueous Media
by
Shi, Qiang-Qiang
,
Xu, Jie
,
Hu, Xiang-Long
in
Annealing
,
Aqueous solutions
,
Biomedical materials
2023
Compared with spherical micelles, rod/worm-like micelles not only have extended blood circulation duration, but also exhibit favorable cellular uptake behavior, which is promising for next-generation nanomedicine and biomaterials. However, the controllable fabrication of narrowly dispersed nanorods in aqueous media is still challenging. Herein, the methodology of thermal annealing was developed for the fabrication of helical nanorods as well as a series of nanorods with different lengths. The thermal annealing process generally consisted of adding a percentage of organic solvent (10%(
V
/
V
) or 20%(
V
/
V
)) to the digital micellar aqueous dispersion, followed by heating at 90 °C for 1 h, then cooling naturally to room temperature, and dialyzing against water to remove the organic solvent. Right-handed helical nanorods were afforded by the treatment of 45 nm digital micelles in the presence of 10%(
V
/
V
) dioxane, while left-handed helical nanorods were obtained in the presence of 20%(
V
/
V
) dioxane. Meanwhile, the controlled growth of rod-like digital micelles was achieved after thermal annealing in the presence of different types of organic solvents, and the length of the annealed nanorods was correlated with the types of organic solvent. Furthermore, no matter the size of initial digital micelles, they all exhibited similar trend of rod growth in the presence of a certain amount of organic solvent, allowing for controllable formulation of narrowly dispersed nanorods. In addition, supramolecular self-assembly by amphiphilic dendritic oligourethane readily fabricated diverse uniform nanorods in aqueous media. Overall, this work provided an attractive methodology to fabricate uniform digital nanorods.
Journal Article
Distribution patterns of Chinese Cixiidae (Hemiptera, Fulgoroidea), highlight their high endemic diversity
by
Luo, Yang
,
Zhang, Jia-Lin
,
Bourgoin, Thierry
in
Agriculture and Forestry
,
Andes region
,
Animalia
2022
Cixiidae are small strictly phytophagous hemipteran insects worldwide distributed. Ecology and systematics of Chinese fauna remains poorly investigated. For instance, does their distribution follows the patterns of biogeogaphical distribution established for their host plants or other related-taxa because they are all obligatory phytophagous taxa? Do they follow the usual distributional Chinese realms and boundaries already recognized? Which zoogeographical Chinese regions and connections between them do they depict. To investigate these issues, we provide here a referenced and comprehensive checklist of the 250 cixiid species currently reported from China (77 new records), with their precise distribution at the regional level. In the 8 Chinese main zoogeographical regions usually recognized and 2 adjacent areas, we analyzed further their diversity at the tribal, generic, and specific levels using a non-metric multidimensional scaling and an unweighted pairwise group analysis using an arithmetic mean cluster analyses. The observed distribution patterns shown that an intercalary Sino-Japanese realm is recognisable between the Palaearctic and Oriental realms. At the regional level, the South China region clusters more closely with the Southwest, Central and North China regions. Taiwan, clearly separated from the South China region and mainland China, is more closely related to the Qinghai-Tibet region and Indochina countries. Although Central and South China regions remain close to each other, the Qinghai-Tibet region appears singularly different.
An updated checklist of the 250 Cixiidae species, known to occur in China and counting for 10% of the Chinese planthopper fauna, is presented based on literature, recent collections, and museum records. More than 400 records distributed among the 28 provinces and 8 regions in China are extensively provided, including 77 new records. Of these, more than 80% of the species (205 species, 82%) have been only reported from China, and most of them are endemic species, which could reflects the great diversity degree of the Chinese regions and local biotypes highlights the uniqueness of this fauna. These species are found in 8 Chinese zoogeographical regions: The Taiwan region is the most diversified with 161 species and the highest rate of endemic species (69.57%), followed by South China (78 species, 17.95%), Central China (60 species, 33.33%), Southwest China (43 species, 39.53%), North China (29 species, 34.48%), Qinghai-Tibet region (10 species, 20%), Northeast China (8 species, 12.5%), and 5 species found in the Inner Mongolia-Xinjiang region that are not endemic ones. Endemism was analyzed for each region and repeated for species distribution patterns across them, 9 being bi-regionally and tri-regionally distributed. The South China-Taiwan pattern is the most richest one, followed by the Central-South China-Taiwan pattern. Semonini and Pentastirini tribes are widespread among all the zoological regions, representing respectively 21.20% and 17.20% of all the species, while Cixiini being is the most common tribe with 45.20%, remains absent from the North-Eastern China region. Andini with only 5.20% of the species is distributed in the Sino-Japanese - Oriental Region; Eucarpini (6.40%) and Borysthenini (2.00%) are mainly concentrated in the south of the Qingling Mountain-Huai River. The remaining four tribes, Bennini (0.40%), Briixini (0.80%), Oecleini (1.20%) and Stenophlepsiini (0.40%) are relatively rare and restricted to Taiwan. At the generic level,
Kuvera
(7.2%) is the most widely distributed genus in China while
Cixius
,
Betacixius
,
Kuvera
,
Oecleopsis
and
Andes
are the more diversified. One genus (
Oliparisca)
is distributed only in the Tibet region, while 10 genera are distributed only in the Taiwan region. In addition, nearly half of the genera (16 genera, 48.48%) are distributed south of the Palearctic/Oriental boundary. A non-metric multidimensional scaling and an unweighted pairwise group method analysis using arithmetic mean clustering based on the Jaccard similarity coefficient matrix support a Palaearctic/Sino-Japanese boundary and a South China region closer to the Southwest, Central and North China regions. The Taiwan region appears clearly separated from the South China region and to mainland China, and more closely related to the Qinghai-Tibet region and Indochina countries. The Central and South China regions appear close to each other, but the Qinghai-Tibet region is singularly isolated.
Journal Article
Effects of walking on epigenetic age acceleration: a Mendelian randomization study
2024
Introduction
Walking stands as the most prevalent physical activity in the daily lives of individuals and is closely associated with physical functioning and the aging process. Nonetheless, the precise cause-and-effect connection between walking and aging remains unexplored. The epigenetic clock emerges as the most promising biological indicator of aging, capable of mirroring the biological age of the human body and facilitating an investigation into the association between walking and aging. Our primary objective is to investigate the causal impact of walking with epigenetic age acceleration (EAA).
Methods
We conducted a two-sample two-way Mendelian randomization (MR) study to investigate the causal relationship between walking and EAA. Walking and Leisure sedentary behavior data were sourced from UK Biobank, while EAA data were gathered from a total of 28 cohorts. The MR analysis was carried out using several methods, including the inverse variance weighted (IVW), weighted median, MR-Egger, and robust adjusted profile score (RAPS). To ensure the robustness of our findings, we conducted sensitivity analyses, which involved the MR-Egger intercept test, Cochran’s
Q
test, and MR-PRESSO, to account for and mitigate potential pleiotropy.
Results
The IVW MR results indicate a significant impact of usual walking pace on GrimAge (BETA = − 1.84, 95% CI (− 2.94, − 0.75)), PhenoAge (BETA = − 1.57, 95% CI (− 3.05, − 0.08)), Horvath (BETA = − 1.09 (− 2.14, − 0.04)), and Hannum (BETA = − 1.63, 95% CI (− 2.70, − 0.56)). Usual walking pace is significantly associated with a delay in epigenetic aging acceleration (EAA) (
P
< 0.05). Moreover, the direction of effect predicted by the gene remained consistent across RAPS outcomes and sensitivity MR analyses. There is a lack of robust causal relationships between other walking conditions, such as walking duration and walking frequency, on EAA (
P
> 0.05).
Conclusion
Our evidence demonstrates that a higher usual walking pace is associated with a deceleration of the acceleration of all four classical epigenetic clocks acceleration.
Key messages
In recent years, observational studies have found that there is a correlation between walking and aging, but the specific relationship is not clear
We used a Mendelian randomization approach to test the causal effect of walking and sedentarism on epigenetic clock acceleration
Mendelian randomization studies have found that faster walking speed may delay physiological aging through causal analysis at the genetic level
Journal Article
Gene expression mediates environmentally induced phenotypic plasticity in Chamaecyparis hodginsii seedlings
by
Wu, Min
,
Chen, Li-Guang
,
Zhang, Jia-Lin
in
Adaptability
,
Chamaecyparis
,
Chamaecyparis hodginsii
2025
In the context of climate change, assessing the adaptive potential of species and populations is crucial for developing effective conservation strategies. Changes in plant gene expression play a significant role in the adaptation process to climate change. This study aims to explore the adaptive responses of the conifer species Chamaecyparis hodginsii (the name has been revised from Fokienia hodginsii ) to climate change and analyze the molecular-level reactions of these long-lived trees to climatic shifts. It seeks to understand their phenotypic responses to climate change, identify key environmental factors driving adaptive gene expression, and provide information for transplantation conservation strategies based on genetic adaptability. By conducting mixed-tissue RNA sequencing on samples from multiple provenances and employing redundancy analysis (RDA), weighted gene co-expression network analysis (WGCNA), and partial least squares path modeling (PLS-PM), the study assesses the impact of climatic variables on gene expression and phenotype. It identifies key gene groups associated with environmental responses and elucidates the complex relationships between environmental factors, functional gene groups, and phenotypic traits. The findings reveal that C. hodginsii adapts to environmental stresses by regulating specific gene activities related to morphological trait adjustments. Moreover, environmental factors such as the impact on tree architecture emphasize the importance of Precipitation Seasonality, Isothermality, and Precipitation of Driest Quarter for adapting to climate stresses. This research not only unveils the complex adaptive responses of C. hodginsii to climate change but also provides critical insights for the management and conservation of long-lived tree species facing climate change threats.
Journal Article
Extraction, purification, characterization, anticoagulant activity, and anticoagulant mechanism of polysaccharides from the heads of Hypomesus olidus
by
Jiang, Guo‐Chuan
,
Zhang, Jia‐Lin
,
Xu, Yu
in
anticoagulant activity
,
anticoagulant mechanism
,
Anticoagulants
2020
The aim of this work was to extract, isolate, and purify polysaccharides from the heads of Hypomesus olidus and to evaluate their anticoagulant activities and anticoagulant mechanisms. Response surface methodology was used to optimize the extraction conditions for ultrasonic‐assisted extraction of polysaccharides from the heads of Hypomesus olidus. The optimal extraction conditions consisted of ultrasonic power of 275 W, ultrasonic time of 50 min, and solid–liquid ratio of 5 ml/g, giving the yield of crude polysaccharides (GYT) of 7.73 ± 0.042%. Three polysaccharide fractions, GYT‐1, GYT‐2, and GYT‐3 were purified from GYT by using DEAE‐cellulose‐52 column and Sephadex G‐100 column for anticoagulant activities. The results showed that two doses (2 and 4 mg/ml) of GYT‐1 and GYT‐3 could significantly prolong (p < .01) in partial thromboplastin time (APTT) (2.19 and 2.37 times, 2.22 and 2.44 times, respectively) and thrombin time (TT) (2.39 and 2.46 times, 2.44 and 2.80 times, respectively) compared with normal control. In particular, GYT‐3 had stronger anticoagulant activity than GYT‐1, and it was composed of arabinose, fructose, glucose, and lactose with molar ratios of 0.595:1: 2.026:0.273. However, GYT‐2 had no anticoagulant activity (p > .05). In addition, anticoagulation mechanism of polysaccharides from the heads of Hypomesus olidus (GYT‐3) was evaluated. The results showed that the anticoagulant activity of GYT‐3 was based on their binding with antithrombin AT‐III. And the inhibitory effects of GYT‐3 on factor IIa and Xa were related to the concentration of AT‐III in plasma. This study may provide a new and promising anticoagulant drug.
The aim of this work was to extract, isolate, and purify polysaccharides from the heads of Hypomesus olidus and to evaluate their anticoagulant activities and anticoagulant mechanisms. The results showed that GYT‐1 and GYT‐3 had significant anticoagulant activities and the anticoagulant activity of Hypomesus olidus head polysaccharides was based on their binding with antithrombin AT‐III. This study may provide a new and promising anticoagulant drug.
Journal Article
Repression of rRNA gene transcription by endothelial SPEN deficiency normalizes tumor vasculature via nucleolar stress
2023
Human cancers induce a chaotic, dysfunctional vasculature that promotes tumor growth and blunts most current therapies; however, the mechanisms underlying the induction of a dysfunctional vasculature have been unclear. Here, we show that split end (SPEN), a transcription repressor, coordinates rRNA synthesis in endothelial cells (ECs) and is required for physiological and tumor angiogenesis. SPEN deficiency attenuated EC proliferation and blunted retinal angiogenesis, which was attributed to p53 activation. Furthermore, SPEN knockdown activated p53 by upregulating noncoding promoter RNA (pRNA), which represses rRNA transcription and triggers p53-mediated nucleolar stress. In human cancer biopsies, a low endothelial SPEN level correlated with extended overall survival. In mice, endothelial SPEN deficiency compromised rRNA expression and repressed tumor growth and metastasis by normalizing tumor vessels, and this was abrogated by p53 haploinsufficiency. rRNA gene transcription is driven by RNA polymerase I (RNPI). We found that CX-5461, an RNPI inhibitor, recapitulated the effect of Spen ablation on tumor vessel normalization and combining CX-5461 with cisplatin substantially improved the efficacy of treating tumors in mice. Together, these results demonstrate that SPEN is required for angiogenesis by repressing pRNA to enable rRNA gene transcription and ribosomal biogenesis and that RNPI represents a target for tumor vessel normalization therapy of cancer.
Journal Article