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2023 Vol. 53, No. 9

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2023-9 Contents
2023, 53(9): 1-2.
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2023-9 Abstract
2023, 53(9): 1-2.
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Life Sciences
The function, structure and dynamic organization of centromeres and kinetochores
Zhen Dou, Ran Liu, Jianye Zang, Xuebiao Yao, Xing Liu
2023, 53(9): 0901. doi: 10.52396/JUSTC-2022-0184
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It is a fundamental task to ensure the faithful transmission of genetic information across generations for eukaryote species. The centromere is a specialized chromosomal region that is essential for mediating sister chromatid alignment and separation during mitosis. Centromere identity is epigenetically determined by nucleosome-containing centromere protein A (CENP-A). The CENP-A nucleosome provides the foundation for the association of the inner kinetochore and the assembly of the outer kinetochore in mitosis. Here we review centromere identity determination, inner kinetochore function and assembly, and outer kinetochore function and assembly. In particular, we focus on the recent advances in the structure-activity relationship of the constitutive centromere-associated network (CCAN). CCAN structure information sheds new light on our understanding of centromere and kinetochore functions and dynamic organization.
Cryopreservation of oocytes: history, achievements and future
Shiyu Zhao, Gang Zhao
2023, 53(9): 0902. doi: 10.52396/JUSTC-2023-0072
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There have been increasing requirements for women’s fertility preservation due to oncological and nononcological reasons in recent years, and meeting these demands will be a hot topic in the coming years. Oocyte cryopreservation is a workable option for preserving women’s fertility, and great advances have already been made and much progress has been made in mammalian gene banking and human oocyte banks. In this paper, we systematically introduce the history of oocyte cryopreservation and vitrification technology and highlight the vitrification carrier. Furthermore, we summarize the fundamentals of oocyte vitrification and discuss the effects of vitrification on oocyte quality. Strategies to improve the effect of oocyte cryopreservation are also proposed. At the end of this review, we conclude oocyte cryopreservation and outline future perspectives.
Modulating miRNA binding sites within circRNA for enhanced translation efficiency
Kewei Zhang, Ge Shan, Liang Chen
2023, 53(9): 0904. doi: 10.52396/JUSTC-2023-0048
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Circular RNAs (circRNAs) are covalently closed circular RNAs, and some of them preserve translation potency. However, modulation of circRNA translation efficiency and its applications need to be explored. In this study, RNAs containing the translation initiation element CVB3 IRES and the coding sequence of luciferase protein were transcribed and circularized in vitro by T7 RNA polymerase and an optimized permutated intron‒exon (PIE) splicing strategy. The circularized RNAs were then transfected and translated into active luciferase in the cultured cells. Insertion of miRNA binding sites at the flanking region of the luciferase coding sequence significantly reduced the translation efficiency of the circRNAs. Mutations of the miRNA binding sites in the firefly luciferase coding sequence led to increased translation efficiency of synthetic circRNAs in cells. We also proved that mutations of the binding sites of specific miRNAs also enhanced the translation efficiency of synthetic circRNAs. Further in vivo experiments via bioluminescence imaging showed that synonymous mutation of the miRNA binding sites promoted synthetic circRNA translation in nude mice. This study demonstrates that the modulation of miRNA binding sites affects the translation efficiency of synthetic circRNAs in vitro and in vivo, which could be used as versatile tools for future applications in clinical imaging.
An abnormal multidrug-resistant and hypervirulent Klebsiella pneumoniae clinical isolate without rmpA or rmpA2
Zhien He, Liwen Cao, Yuanyuan Dai, Huaiwei Lu, Baolin Sun, Yujie Li
2023, 53(9): 0905. doi: 10.52396/JUSTC-2023-0085
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Klebsiella pneumoniae is a notorious opportunistic pathogen, especially hypervirulent K. pneumoniae (hvKp). Fortunately, most classical hvKp strains are antibiotic-susceptible. However, in recent years, reports of multidrug-resistant hvKp (MDR-hvKp) have increased dramatically, threatening the health and safety of people worldwide. Here, we report the discovery of MDR-hvKp without rmpA and rmpA2 in a 92-year-old patient with chronic obstructive pulmonary disease. The patient died on the eighth day of hospitalization. Phenotyping experiments and whole-genome sequencing of K. pneumoniae isolate 21072329 isolated from the patient’s sputum were performed. Moreover, 21072329 belongs to ST11-KL47 MDR-hvKp, which was highly lethal to Galleria mellonella. Meanwhile, 21072329 had a strong viscosity, and it was difficult to completely centrifuge it; 21072329 carried ESBL genes (blaCTX-M-65, blaSHV-158, and blaTEM-1) and a carbapenemase gene (blaKPC-2), and it was resistant to carbapenem antibiotics and third- and fourth-generation cephalosporins. Although 21072329 had the characteristics of hvKp, rmpA and rmpA2 could not be found in its genome; it also only carried a siderophore of yersiniabactin. This may indicate that other hypervirulence factors promote the formation of hvKp. MDR-hvKp has already brought an enormous burden to global medical care, and those carrying unknown hypervirulence factors are new threats, so urgent prevention and control with research are urgently needed.
Dynamics in the assembly of the 30S ribosomal subunit investigated by coarse-grained simulations
Xin Liu, Zhiyong Zhang
2023, 53(9): 0906. doi: 10.52396/JUSTC-2023-0064
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The ribosome is a large biomolecular complex responsible for protein synthesis. In Escherichia coli (E. coli), a complete ribosome is composed of a 30S small subunit and a 50S large subunit. For approximately half a century, the 30S subunit has been a key model system for studying the in vitro assembly of the ribosome, and an assembly map has been proposed. However, structural details in the assembly of this protein‒RNA complex remain elusive. In this paper, we conducted a series of coarse-grained simulations following the order of the assembly map to investigate conformational dynamics during the assembly process of the 30S subunit. It has been found that the tertiary structure of naked 16S rRNA is very unstable, which is the case after binding of early-assembly proteins. The mid-assembly proteins can significantly restrict the mobility of the 16S rRNA and make the latter close to the native structure. The final binding of the late-assembly proteins would fully obtain the collective motion of the 16S rRNA. In particular, proteins S9 and S3 may have more important contributions to the assembly of the 30S subunit than other S proteins. Our strategy of coarse-grained simulations can be generally used to study assembly dynamics of large biomolecular complexes as long as the assembly map is available.
Article
Construction of an M1 macrophage-related lncRNA signature for predicting the tumor immune microenvironment
Qi Wu, Yiming Liu, Qingsong Hu, Huihui Wu
2023, 53(9): 0903. doi: 10.52396/JUSTC-2022-0185
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Long noncoding RNAs (lncRNAs) are considered crucial molecules associated with the tumor microenvironment (TME) and tumor immune microenvironment (TIM). Macrophages are important members of the immune system, and M1 macrophage function-associated lncRNAs still need to be further investigated. In this study, a lncRNA signature was constructed based on transcriptome differences between high and low M1 macrophage infiltration cohorts. This lncRNA signature included seven lncRNAs: LINC01494, ZDHHC20-IT1, LINC01450, LINC00871, EVX1-AS, KIF25-AS and AADACL2-AS1, and all of them were upregulated in patients lacking M1 macrophages, indicating their roles in inhibiting macrophage infiltration and polarizing to the M1 subtype, leading to an immune exclusion TME, which has been demonstrated to be closely correlated with poor prognosis. This lncRNA signature not only predicted undesirable clinical outcomes but was also associated with the immunosuppressive environment of the tumor region, which is mediated by hindering antigen presentation and processing progress. In addition, the predictive value of this lncRNA signature for immune checkpoint inhibition (ICI) therapy was also evaluated, which further enriched and strengthened the power of lncRNAs in predicting the immunotherapy response rate.

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