The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum)

Zanthoxylum armatum and Zanthoxylum bungeanum, known as ‘Chinese pepper’, are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.     

采伐剩余物管理对杉木人工林土壤nosZ型反硝化细菌群落多样性的影响

反硝化细菌是土壤氧化亚氮(N₂O)排放的关键因子。以杉木人工林为研究对象,设置4种采伐剩余物处理方式(RF:对照;RB:火烧;MT:粉碎;NR:移除),采用高通量测序技术,以nosZ为标记基因,测定了自2018年9月—2020年9月,2年期间土壤nosZ型反硝化细菌群落的组成和丰度。研究结果显示,4种采伐剩余物处理中的土壤nosZ型反硝化细菌90%以上来自变形菌门,优势菌属包括固氮螺菌属、中慢生根瘤菌属、动胶菌属、伯克霍尔德菌属、嗜酸菌属、慢生根瘤菌属、假单胞菌属、固氮弧菌属以及无色杆菌属;样本间差异物种的显著性分析表明,在处理完成半年时,火烧相较于对照于β-变形菌纲水平显著增加了nosZ基因丰度;在处理完成一年时,火烧分别于红螺菌目、红螺菌科、固氮螺菌属水平显著高于粉碎;粉碎相较于移除在处理完成一年时,于γ-变形菌纲和产碱菌科水平显著增加了nosZ基因丰度;在处理完成两年时,粉碎处理的nosZ基因丰度在变形菌门水平显著高于对照和火烧。α多样性数据显示,处理完成一年时,粉碎处理相较于对照和移除显著增加了Shannon和Simpson指数;处理完成两年时,粉碎和火烧...     

中国仓鼠卵巢细胞表观遗传调控研究进展

中国仓鼠卵巢(Chinese hamster ovary, CHO)细胞因其具有可悬浮培养及进行蛋白质糖基化等翻译后修饰等优势,在生物制药重组蛋白生产方面具有不可替代的重要作用。但转基因沉默、表观遗传修饰等影响基因表达调控,造成CHO细胞表达稳定性降低而导致重组蛋白产量下降。本文对CHO细胞中表观遗传修饰包括DNA甲基化、组蛋白修饰和miRNA的作用研究,以及对基因表达调控的影响进行了综述。     

大白菜NHX基因家族的鉴定与表达分析

Na+/H+逆向转运蛋白(Na+/H+antiporter,NHX)基因家族在植物响应盐胁迫中发挥重要作用。本研究鉴定了大白菜NHX基因家族成员,并分析了大白菜NHX基因(Brassica rapa ssp.Pekinensis NHX,BrNHXs)响应高温、低温、干旱和盐胁迫等非生物逆境的表达模式。结果表明,在大白菜中共鉴定到9个NHX基因家族成员,分布在大白菜的6条染色体上,其氨基酸数目在513–1154 aa之间,相对分子量集中在56804.22–127856.66 kDa,等电点位于5.35–7.68之间。该基因家族成员主要存在于液泡中,基因结构完整,外显子的数目介于11–22之间。大白菜NHX基因家族编码的蛋白质二级结构都具有α-螺旋、β-转角和不规则卷曲结构,其中α-螺旋发生频率较高。实时荧光定量PCR(quantitative real-time PCR,qRT-PCR)分析显示,该基因家族成员在高温、低温、干旱和盐胁迫下均有不同程度地响应,且在不同时间表达差异显著。以BrNHX02和BrNHX09对这4种胁迫的响应最为显著,表达量在处理72 h时均显著上调,可作为候选基因进一步验证其功能。     

High-efficiency and multilocus targeted integration in CHO cells using CRISPR-mediated donor nicking and DNA repair inhibitors

Efforts to leverage clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) for targeted genomic modifications in mammalian cells are limited by low efficiencies and heterogeneous outcomes. To aid method optimization, we developed an all-in-one reporter system, including a novel superfolder orange fluorescent protein (sfOrange), to simultaneously quantify gene disruption, site-specific integration (SSI), and random integration (RI). SSI strategies that utilize different donor plasmid formats and Cas9 nuclease variants were evaluated for targeting accuracy and efficiency in Chinese hamster ovary cells. Double-cut and double-nick donor formats significantly improved targeting accuracy by 2.3–8.3-fold and 19–22-fold, respectively, compared to standard circular donors. Notably, Cas9-mediated donor linearization was associated with increased RI events, whereas donor nicking minimized RI without sacrificing SSI efficiency and avoided low-fidelity outcomes. A screen of 10 molecules that modulate the major mammalian DNA repair pathways identified two inhibitors that further enhance targeting accuracy and efficiency to achieve SSI in 25% of transfected cells without selection. The optimized methods integrated transgene expression cassettes with 96% efficiency at a single locus and with 53%–55% efficiency at two loci simultaneously in selected clones. The CRISPR-based tools and methods developed here could inform the use of CRISPR/Cas9 in mammalian cell lines, accelerate mammalian cell line engineering, and support advanced recombinant protein production applications.     

Study on TFF1 and PALB2 gene variants associated with gastric carcinoma risk in the Chinese Han population

ObjectiveGastric carcinoma (GC) has received extensive attention due to its complex pathogenesis. Studies have shown that the expression of Trefoil factor 1 (TFF1) and Partner and localiser of BRCA2 (PALB2) genes promotes the occurrence of GC. Therefore, we investigated whether TFF1 and PALB2 gene polymorphisms are associated with GC risk in the Chinese Han population.MethodsA total of 509 GC cases and 505 controls were recruited, and single nucleotide polymorphisms (SNPs) of TFF1 and PALB2 in these subjects were genotyped. The association between each candidate polymorphism and GC risk was assessed by calculating odds ratios (ORs) and 95% confidence intervals (CIs). The visualization of gene-gene interactions and functional enrichment analysis were then performed using Cytoscape software and the R package “cluster profile”.ResultsThe TFF1 rs2156310 polymorphism significantly reduced the predisposition to GC in people under 60 years of age (AA vs. AG - GG, OR = 0.58, 95% CI = 0.35–0.97, p = 0.036). The gender-stratified analysis found that PALB2 rs513313 was significantly associated with the risk of GC in males (CT vs. TT, OR = 1.51, 95% CI = 1.06–2.15, p = 0.022). Besides, PALB2 rs249954 significantly reduced the susceptibility to GC in females (AA vs GG, OR = 0.42, 95% CI = 0.19–0.94, p = 0.034).ConclusionOur results revealed that TFF1 and PALB2 gene polymorphisms were correlated with the genetic susceptibility to GC, providing certain data support for researchers to further study the mechanism of GC.     

2种中草药对福寿螺的杀灭效果及对肝脏影响

【目的】有效控制福寿螺产生的危害,为实现中草药的资源化利用提供依据。【方法】以甘草、陈皮为植物源灭螺剂,进行不同浓度梯度(0、0.5、1.5、3.0、4.5、6.0 g·L^-1)提取液浸泡下的灭螺活性探究。【结果】甘草组、陈皮组处理下福寿螺死亡率随时间的增长在不同浓度下毒杀效果明显。对48 h时福寿螺死亡率数据进行概率单位法回归分析,发现甘草组(LC₂₅、LC₅₀、LC₇₅)<陈皮组(LC₂₅、LC₅₀、LC₇₅),说明福寿螺对甘草更敏感。为进一步探究福寿螺死亡原因,在前期研究的基础上深入探讨甘草、陈皮提取液对福寿螺的肝脏的影响,在亚致死浓度甘草0.511 g·L^-1 (LC₂₅)、0.940 g·L^-1 (LC₅₀)、1.727 g·L^-1 (LC₇₅)和陈皮3.892 g·L^-1 (LC₂₅)、4.863 g·L^-1 (LC₅₀)、6.076 g·L^-1 (LC₇₅)处理下对福寿螺肝脏进行扫描电镜观察,结果表明,相比对照组,处理组福寿螺肝脏组织表面干瘪,失去水分,受损严重时,质地松散,表面组织脱落。【结论】2种植物提取液均可以较好地灭杀福寿螺,且严重破坏福寿螺核心组织肝脏,甘草、陈皮可作为植物源灭螺剂进一步研究开发利用。     

放散式体外冲击波穴位治疗联合中药熏洗治疗老年膝骨关节炎的疗效分析

摘要 目的：评价放散式体外冲击波（rESW）穴位治疗联合中药熏洗在老年膝骨关节炎（KOA）中的应用效果。方法：选入2021年2月~2022年8月我院收治的老年KOA患者76例,根据治疗方法不同分为对照组和观察组,各38例,两组均予以中药熏洗,观察组加用rESW穴位治疗。评价两组的治疗效果、膝关节功能、疼痛程度等指标,并进行统计比较。结果：与治疗前相比,两组治疗2周、治疗4周时的VAS评分明显下降（P＜0.05）,而观察组下降幅度更大,与对照组差异显著（P＜0.05）;两组治疗前Lysholm评分无明显差异（P＞0.05）,而观察组治疗2周、治疗4周时的Lysholm评分显著高于对照组（P＜0.05）;观察组治疗显效率和有效率均显著高于对照组（P＜0.05）;观察组治疗2周、4周时的血清IL-1β、TNF-α和MMP-13水平较对照组低（P＜0.05）。结论：rESW穴位联合中药熏洗治疗老年KOA患者疗效显著,可缓解疼痛症状,改善膝关节功能,控制炎症反应,且操作简单,值得推荐。     

Comparison of mechanistic and hybrid modeling approaches for characterization of a CHO cultivation process: Requirements,pitfalls and solution paths

Despite the advantages of mathematical bioprocess modeling, successful model implementation already starts with experimental planning and accordingly can fail at this early stage. For this study, two different modeling approaches (mechanistic and hybrid) based on a four-dimensional antibody-producing CHO fed-batch process are compared. Overall, 33 experiments are performed in the fractional factorial four-dimensional design space and separated into four different complex data partitions subsequently used for model comparison and evaluation. The mechanistic model demonstrates the advantage of prior knowledge (i.e., known equations) to get informative value relatively independently of the utilized data partition. The hybrid approach displayes a higher data dependency but simultaneously yielded a higher accuracy on all data partitions. Furthermore, our results demonstrate that independent of the chosen modeling framework, a smart selection of only four initial experiments can already yield a very good representation of a full design space independent of the chosen modeling structure. Academic and industry researchers are recommended to pay more attention to experimental planning to maximize the process understanding obtained from mathematical modeling.