Epitranscriptomic technologies and analyses

RNA can interact with RNA-binding proteins(RBPs), mRNA, or other non-coding RNAs(ncRNAs) to form complex regulatory networks. High-throughput CLIP-seq, degradome-seq, and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions. However, assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins(RBPs) remains technically challenging. Chemical modifications to mRNA also play important roles in regulating gene expression. Investigation of the functional roles of these modifications relies highly on the detection methods used. RNA structure is also critical at nearly every step of the RNA life cycle. In this review, we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs. We also summarize methods used to detect RNA modifications and to probe RNA structure.     

Epidermal growth factor improves intestinal morphology by stimulating proliferation and differentiation of enterocytes and mTOR signaling pathway in weaning piglets

Epidermal growth factor(EGF) has been shown to improve piglet intestinal morphology and epithelial recovery. In an attempt to further understand the mechanisms behind these improvements, this study tested the hypothesis that dietary EGF may affect intestinal morphology by stimulating the proliferation and differentiation of enterocytes in weaning piglets. In piglets receiving200 μg kg–1 EGF, crypt depth and villus height increased(P0.05). Adding 400 μg kg–1 EGF increased villus height-to-crypt depth ratio(P0.05), but reduced crypt depth(P0.05). Dietary supplementation with 200 μg kg–1 EGF significantly increased the number of Ki67-positive cells(P0.01) and tended to increase the mRNA level of proliferating cell nuclear antigen(P0.10).However, this supplementation decreased the expression level of intestinal fatty acid-binding protein(P0.05). Piglets fed with400 μg kg–1 EGF had an increased mRNA level of intestinal alkaline phosphatase(P0.05). The phosphorylation of m TOR(mammalian target of rapamycin) was observed in the 200 μg kg–1 EGF group. These results suggest that dietary supplementation with a low level of EGF improved piglet intestinal morphology through stimulating the proliferation and differentiation of enterocytes, and the mTOR signaling pathway may partly be involved in this process.     

Nanopore sequencing of African swine fever virus

正Dear Editor,African swine fever (ASF) is one of the most pathogenic viral diseases in pigs caused by African swine fever virus(ASFV). The fatality rate is almost 100%, which brings huge economic losses to the hog industry in countries with epi-     

Distinct lung microbial community states in patients with pulmonary tuberculosis

An improved understanding of the lung microbiome may lead to better strategies to diagnose, treat, and prevent pulmonary tuberculosis(PTB). However, the characteristics of the lung microbiomes of patients with TB remain largely undefined. In this study, 163 bronchoalveolar lavage(BAL) samples were collected from 163 sputum-negative suspected PTB patients. Furthermore, 12 paired BAL samples were obtained from 12 Mycobacterium tuberculosis-positive(MTB+) patients before and after negative conversion following a two-month anti-TB treatment. The V3–V4 region of the 16 S ribosomal RNA(rRNA) gene was used to characterize the microbial composition of the lungs. The results showed that the prevalence of MTB in the BAL samples was 42.9%(70/163) among the sputum-negative patients. The α-diversity of lung microbiota was significantly less diverse in MTB+ patients compared with Mycobacterium tuberculosis-negative(MTB–) patients. There was a significant difference in β-diversity between MTB+ and MTB– patients. MTB+ patients were enriched with Anoxybacillus, while MTB– patients were enriched with Prevotella, Alloprevotella, Veillonella, and Gemella. There was no significant difference between the Anoxybacillus detection rates of MTB+ and MTB– patients. The paired comparison between the BAL samples from MTB+ patients and their negative conversion showed that BAL negative-conversion microbiota had a higher α-diversity. In conclusion, distinct features of airway microbiota could be identified between samples from patients with and without MTB. Our results imply links between lung microbiota and different clinical groups of active PTB.     

Molecular diversity of the 5S nuclear ribosomal DNA in Campeiostachys with StHY haplome constitution

To detect the genomic constitutions and investigate the evolutionary relationships between Campeiostachys Drobov and Elymus L. species, we have cloned and analyzed 271 5S nuclear ribosomal DNA sequences from 27 accessions of these species, mostly of Chinese origin. We identified Long H1, Short S1, and Long Y1 unit classes in nine Campeiostachys or Elymus species. The identification of the three orthologous unit classes was confirmed by the neighbor‐joining tree of each unit class from PAUP and the phylogeny tree of three unit classes from MrBayes. The results suggested that these Elymus species comprise StYH haplomes and should be included in Campeiostachys. The phylogeny tree showed a clear separation between the S1 unit class and Y1 unit class. However, Y1 unit class sequences formed a sister clade to the S1 unit class, implying that although the St and Y haplomes might have some affinity, they are distinct from one another. The phylogeny tree also indicated that the five species in sect. Turczaninovia (C. dahurica var. cylindrica, C. dahurica var. dahurica, C. dahurica var. tangutorum, E. purpuraristatus, and E. dahuricus Turcz. ex Griseb. var. violeus C. P. Wang & H. L. Yang) might share a more recent common ancestor, whereas the four species in sect. Elymus (C. nutans, E. breviaristatus (Keng) Keng ex Keng f., E. sinosubmuticus (Keng) Keng f., and E. atratus (Nevski) Hand.‐Mazz.) share a close relationship. By identifying only one type of unit class for each haplome, we propose that the 5S nuclear ribosomal DNA sequences of species within Campeiostachys might have undergone haplome‐specific concerted evolution.     

阿加曲班对MCAO大鼠不同时间点血小板功能的影响

建立大脑中动脉闭塞(model of middle cerebral artery occlusion,MCAO)大鼠模型,研究阿加曲班对大鼠不同时间脑缺血再灌注损伤血小板功能的影响。将120只健康雄性SD大鼠随机分为假手术组(Sham)、模型组(Model)和阿加曲班给药组(Argatroban),其中Argatroban组分为4组:Argatroban+30 min组、Argatroban+1 h组、Argatroban+3 h组和Argatroban+7 h组,Sham组和Model组40只,其余各组每组10只。线栓法制备大鼠MCAO模型,术中输注Argatroban,剂量为0.3μg·kg^-1·min^-1,完成手术前5 min停止输注。手术完成后,Sham组和Model组分别于术后30 min、1 h、3 h和7 h处死10只取样;Argatroban给药组5个时间点处死取样。检测大鼠血浆血细胞数量,并计数骨髓有核细胞数的变化。采用流式细胞仪检测血小板-白细胞聚集体(platelet-leukocyte aggregates,PLA)表达水平,观察活化部分凝血活酶时间(activated partial thromboplastin time,APTT)、血小板计数变化,ELISA检测血浆D-二聚体和TAT。结果显示,与Sham组相比,Model组大鼠的红细胞(RBC)、白细胞(WBC)、血红蛋白含量(HGB)和中性粒细胞(GR)数都显著升高(p<0.05),且与给药组没有统计学差异。Sham组、Model组和Argatroban给药组的骨髓有核细胞数也没有统计学差异。与Sham组相比,Model组PLA表达水平极显著升高(p<0.01),Argatroban+30 min组PLA表达水平却低于Sham组,但没有统计学差异,Argatroban+1 h组高于Sham组和Argatroban+30 min组(p<0.05),Argatroban+3 h组和Argatroban+7 h组高于Argatroban+1 h组低于Sham组。术后各组的血小板计数均高于Sham组(p<0.05),Argatroban各组的血小板计数要低于Model组(p<0.05),并在30 min时达到最低,30 min以后血小板升高,但是1 h以后血小板不再升高,趋于稳定。Argatroban各组PT和APTT虽略有降低,但是与Sham组和Model组并没有统计学差异。造模后各组TAT、D-二聚体水平显著升高,Argatroban各组TAT水平较模型组明显降低(p<0.05),Argatroban+30 min组水平最低。MCAO模型大鼠血液呈现高凝状态,凝血功能和纤维蛋白溶解功能亢进,血小板活化增强,阿加曲班可对此起到改善作用。