Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation

Although the Trithorax histone methyltransferases ATX1–5 are known to regulate development and stress responses by catalyzing histone H3K4 methylation in Arabidopsis thaliana, it is unknown whether and how these histone methyltransferases affect DNA methylation. Here, we found that the redundant ATX1–5 proteins are not only required for plant development and viability but also for the regulation of DNA methylation. The expression and H3K4me3 levels of both RNA-directed DNA methylation (RdDM) genes (NRPE1, DCL3, IDN2, and IDP2) and active DNA demethylation genes (ROS1, DML2, and DML3) were downregulated in the atx1/2/4/5 mutant. Consistent with the facts that the active DNA demethylation pathway mediates DNA demethylationmainly at CG and CHG sites, and that the RdDM pathway mediates DNA methylation mainly at CHH sites, whole-genome DNA methylation analyses showed that hyper-CG and CHG DMRs in atx1/2/4/5 significantly overlapped with those in the DNA demethylation pathway mutant ros1 dml2 dml3 (rdd), and that hypo-CHH DMRs in atx1/2/4/5 significantly overlapped with those in the RdDM mutant nrpe1, suggesting that the ATX paralogues function redundantly to regulate DNA methylation by promoting H3K4me3 levels and expression levels of both RdDM genes and active DNA demethylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex components function as a whole to regulate DNA methylation. This study reveals a previously uncharacterized mechanism underlying the regulation of DNA methylation.     

四川格西沟国家级自然保护区鸟类多样性初探

鸟类多样性研究是国家级自然保护区的重要工作。2020年6月—2021年5月,采用样线法和样点法,调查了四川格西沟国家级自然保护区的鸟类多样性。结果显示:结合历史文献资料,保护区共有鸟类19目56科249种。其中,国家一级重点保护动物10种,国家二级重点保护动物35种,中国特有种11种。居留型以留鸟为主,共156种(62.65%),其次是夏候鸟60种(24.10%)、旅鸟19种(7.63%)、冬候鸟14种(5.62%)。区系组成以东洋界为主,共116种(46.59%),古北界103种(41.37%)、广布种30种(12.04%)。各生态系统中森林和灌丛生态系统Shannon-Wiener指数最高,其他生态系统最低,森林和灌丛生态系统的Sorenson相似性指数最高;夏、秋季的Shannon-Wiener指数和Pielou均匀度指数最高,冬季最低。建议保护区建立长期监测体系,并持续开展鸟类保护宣传活动,加大巡护和管控力度,降低保护区内的人为干扰,同时注重鸟类所利用栖息地的保护。     

云南省爬行动物名录和地理区划更新

云南省作为中国生物多样性最高的省份, 其详实的物种本底资料对我国生物多样性研究和保护具有重要意义。本文在前期研究的基础上, 结合实体标本, 汇总编制了云南省现生、原生爬行动物更新名录。截至2021年12月31日, 云南省记录爬行动物25科82属235种, 其中龟鳖目4科12属16种, 有鳞目蜥蜴亚目6科20属72种, 蛇亚目15科50属147种。较《云南两栖爬行动物》确认新增82种, 存疑收录21种, 移除23种。基于先前云南省爬行动物区划和更新后的物种分布信息, 将云南省爬行动物地理分为6个动物地理区, 即滇西北横断山区、滇西山地区、滇南山地区、滇东南山地区、滇中高原区以及滇东北山地区; 其中滇西北横断山区、滇西山地区、滇中高原区和滇东南山地区的范围与先前研究相比有所调整。结合调整后的爬行动物地理区划, 对物种分布、物种特有性、受威胁状况等给出了统计结果。云南省爬行动物特有物种、国内仅见于云南的非特有物种数量较多, 受威胁等级高。建议今后继续加大分类学研究投入, 对滇西北、滇中特有爬行动物分布集中的区域积极开展栖息地保护工作, 同时在最新调整的《国家重点保护野生动物名录》基础上, 定期组织专家研讨, 对《云南省省级重点保护动物名录》提出更新建议。     

微生物相互作用中的空间自组织

微生物在全球生态系统中占据着重要地位, 其中一个重要的研究领域是微生物与环境(包括无机环境与生物环境)之间的相互作用。在生态相互作用过程中, 微生物常常通过自组织形成特定的空间模式。微生物的空间模式在种群稳定性、群落动态变化以及维持合作行为方面具有重要作用。本文中, 我们梳理了当下对微生物空间自组织及其所形成的空间模式的研究内容, 首先介绍什么是空间自组织, 再根据生态相互作用类型对自组织的空间模式进行描述, 其中重点讨论合作与竞争中的空间模式, 接着关注微生物空间自组织的过程, 最后我们指出空间自组织对整个群体的结构和功能稳定具有重要意义。研究微生物种群间相互作用中的空间模式, 有助于探索维持合作行为的新机制, 进而为微生物共生系统的构建提供新的理解。     

Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants

Highlights
1 Deletion of residues 156–157 warps the neighboring beta-sheet and leads NTD and RBD to shift.
2 T859N stabilizes the packing of the 630 loop motif to make RBD standing transition more difficult.
3 The overall structures of the closed state S complex from different variants resemble each other.
4 Mutations in FPPR may affect the overall structure of the trimeric spike protein.     

EA15, MIR22, LINC00472 as diagnostic markers for diabetic kidney disease

This study aimed to investigate the molecular mechanisms of diabetic kidney disease (DKD) and to explore new potential therapeutic strategies and biomarkers for DKD. First we analyzed the differentially expressed changes between patients with DKD and the control group using the chip data in Gene Expression Omnibus (GEO) database. Then the gene chip was subjected to be annotated again, so as to screen long noncoding RNAs (lncRNAs) and study expression differences of these lncRNAs in DKD and controlled samples. At last, the function of the differential lncRNAs was analyzed. A total of 252 lncRNAs were identified, and 14 were differentially expressed. In addition, there were 1,629 differentially expressed messenger RNAs (mRNAs) genes, and proliferation and apoptosis adapter protein 15 (PEA15), MIR22, and long intergenic nonprotein coding RNA 472 ( LINC00472) were significantly differentially expressed in DKD samples. Through functional analysis of the encoding genes coexpressed by the three lncRNAs, we found these genes were mainly enriched in type 1 diabetes and autoimmune thyroid disease pathways, whereas in Gene Ontology (GO) function classification, they were also mainly enriched in the immune response, type I interferon signaling pathways, interferon-γ mediated signaling pathways, and so forth. To summary, we identified EA15, MIR22, and LINC00472 may serve as the potential diagnostic markers of DKD.     

Thioredoxin-interacting protein deficiency alleviates phenotypic alterations of podocytes via inhibition of mTOR activation in diabetic nephropathy

Thioredoxin-interacting protein (TXNIP) is induced by high glucose (HG), whereupon it acts to inhibit thioredoxin, thereby promoting oxidative stress. We have found that TXNIP knockdown in human renal tubular cells helped prevent the epithelial-to-mesenchymal transition (EMT). Here, we studied the potential effect of TXNIP on podocyte phenotypic alterations in diabetic nephropathy (DN) in vivo and in vitro. In conditionally immortalized mouse podocytes under HG conditions, knocking down TXNIP disrupted EMT, reactive oxygen species (ROS) production, and mammalian target of rapamycin (mTOR) pathway activation. Further, Raptor short hairpin RNA (shRNA), Rictor shRNA, and mTOR specific inhibitor KU-0063794 were used to assess if the mTOR signal pathway is involved in HG-induced EMT in podocytes. We found that Raptor shRNA, Rictor shRNA, and KU-0063794 could all restrain HG-induced EMT and ROS production in podocytes. In addition, antioxidant Tempol or N-acetylcysteine presented a prohibitive effect on HG-induced EMT in podocytes. Streptozotocin was utilized to render equally diabetic in wild-type (WT) control and TXNIP ^−/− (TKO) mice. Diabetes did not increase levels of 24-hr urinary protein, serum creatinine, blood urea nitrogen, and triglyceride in TXNIP ^−/− mice. Podocyte phenotypic alterations and podocyte loss were detected in WT but not in TKO diabetic mice. Oxidative stress was also suppressed in diabetic TKO mice relative to WT controls. Also, TXNIP deficiency suppresses the activation of mTOR in glomeruli of streptozotocin-induced diabetic mice. Moreover, TXNIP expression, mTOR activation, Nox1, and Nox4 could be detected in renal biopsy tissues of patients with DN. This suggests that decreased TXNIP could ameliorate phenotypic alterations of podocytes via inhibition of mTOR in DN, highlighting TXNIP as a promising therapeutic target.     

MicroRNA miR-505-5p Promotes Oxygen-Glucose Deprivation/Reoxygenation-Induced Neuronal Injury via Negative Regulation of CREG1 in Cultured Neuron-Like Cells

Neurophysiology - Cerebral ischemia/reperfusion (I/R) injury is associated with various cardiovascular and cerebrovascular diseases with high disability, morbidity, and mortality rates. MicroRNAs...