Ophthalmic manifestations have recently been observed in acute and post-acute complications of COVID-19 caused by SARS-CoV-2 infection. Our precious study has shown that host RNA editing is linked to RNA viral infection, yet ocular adenosine to inosine (A-to-I) RNA editing during SARS-CoV-2 infection remains uninvestigated in COVID-19. Herein we used an epitranscriptomic pipeline to analyze 37 samples and investigate A-to-I editing associated with SARS-CoV-2 infection, in five ocular tissue types including the conjunctiva, limbus, cornea, sclera, and retinal organoids. Our results revealed dramatically altered A-to-I RNA editing across the five ocular tissues. Notably, the transcriptome-wide average level of RNA editing was increased in the cornea but generally decreased in the other four ocular tissues. Functional enrichment analysis showed that differential RNA editing (DRE) was mainly in genes related to ubiquitin-dependent protein catabolic process, transcriptional regulation, and RNA splicing. In addition to tissue-specific RNA editing found in each tissue, common RNA editing was observed across different tissues, especially in the innate antiviral immune gene MAVS and the E3 ubiquitin-protein ligase MDM2. Analysis in retinal organoids further revealed highly dynamic RNA editing alterations over time during SARS-CoV-2 infection. Our study thus suggested the potential role played by RNA editing in ophthalmic manifestations of COVID-19, and highlighted its potential transcriptome impact, especially on innate immunity.

Background Changshun green-shell laying hens are unique to the Guizhou Province, China, and have high egg quality but relatively low yield. Egg production traits are regulated by the hypothalamus-pituitary-ovary axis. However, the underlying mechanism remains unclear. Thus, we conducted RNA sequencing of hypothalamic and pituitary tissues from low- and high-yielding Changshun green-shell laying hens to identify critical pathways and candidate genes involved in controlling the egg production rate. Results More than 39 million clean reads per sample were obtained, and more than 82% were mapped to the Gallus gallus genome. Further analysis identified 1,817 and 1,171 differentially expressed genes (DEGs) in the hypothalamus and pituitary, respectively. Nineteen DEGs were upregulated in both the hypothalamus and pituitary of high-yielding chickens. The functions of these DEGs were mainly associated with ion transport or signal transduction. Gene set enrichment analysis revealed that the pathways enriched in the hypothalamus were mainly associated with gonadotropin-releasing hormone (GnRH) secretion, neurotransmitter release, and circadian rhythms. The pathways enriched in the pituitary were mainly associated with GnRH secretion, energy metabolism, and signal transduction. Five and four DEGs in the hypothalamus and pituitary, respectively, were selected randomly for qRT-PCR analysis. The expression trends determined via qRT-PCR were consistent with the RNA-seq results. Conclusions The current study identified 19 DEGs upregulated in both the hypothalamus and pituitary gland, which could provide an important reference for further studies on the molecular mechanisms underlying egg production in Changshun green-shell laying hens. In addition, enrichment analysis showed that GnRH secretion and signal transduction, especially neurotransmitter release, play crucial roles in the regulation of egg production.

In order to study the effects of ecological chicken farming on soil physicochemical properties and microflora structure in karst mountains, soil samples were collected from farming area（CA group）, rotation area（RA group） and non-farming area（NCA group）, and the pH value, moisture content, bulk density, total nitrogen, total phosphorus, total potassium and microbial composition were analyzed. The results showed that compared with NCA group, the soil pH value of CA group extremely significantly decreased, the moisture content significantly decreased, and the total potassium and total phosphorus contents significantly or extremely significantly increased. The bacterial Alpha diversity indexes（Ace, Chao1, Shannon, Simpson index） of CA group was the lowest; compared with CA group, the Alpha diversity index of RA group increased significantly or extremely significantly. The fungal Shannon index was the lowest in CA group, while that in RA group was the highest. Compared with CA and NCA groups, the Ace index and Chao1 index in RA group increased significantly or extremely significantly. The dominant bacterial phyla of the three groups were Proteobacteria（36.452%～42.378%）, Acidobacteria（23.362%～31.836%） and Bacteroidetes（4.710%～11.488%）; the dominant fungal phyla were Ascomycetes（17.453%～31.368%）, Basidiomycetes（13.295%～19.737%） and Mucorhyta（7.253%～21.492%）. Soil pH value and total nitrogen content extremely significantly or significantly affected the bacterial community structure; total potassium content and bulk density significantly affected the fungal community structure. In summary, continuous chicken farming in karst mountains could lead to soil acidification, weakening of water holding capacity, increase of potassium and phosphorus content, and decrease of bacterial richness and diversity and fungal diversity; the above situations could be improved after rest rotation.

研究旨在明确长顺绿壳蛋鸡肠道菌群结构及功能.健康、体重无差异的20只27周龄长顺绿壳蛋鸡饲养35 d,随机选择4只,分别提取十二指肠、回肠和盲肠内容物的微生物总DNA,对16S rRNA进行高通量测序.结果显示:盲肠OTUs个数最多,其次为回肠,最少为十二指肠.盲肠的Ace指数、Chao-1指数和Shannon指数极显著高于十二指肠和回肠(P<0.01).回肠的Ace指数和Chao-1指数显著高于十二指肠(P<0.05).在门水平上,厚壁菌门为十二指肠(97.06％)和回肠(96.36％)的优势菌门;拟杆菌门(62.55％)和厚壁菌门(34.05％)为盲肠的优势菌门.在属水平上,乳杆菌属为十二指肠(94.133％)和回肠(95.273％)的优势菌属;拟杆菌属为盲肠(40.548％)的优势菌属.PICRUSt功能预测显示,肠道微生物基因主要富集于KEGG的新陈代谢(44.74％～49.34％)通路,其中盲肠营养物质代谢相关通路中富集基因相对丰度较高,如氨基酸代谢、能量代谢以及辅因子与维生素代谢等.研究表明,随着长顺绿壳蛋鸡肠道延伸,菌群多样性程度明显增加,且盲肠菌群的营养代谢作用更为活跃.