A Prognostic Model to Predict Recovery of COVID-19 Patients Based on Longitudinal Laboratory Findings

Virologica Sinica - The temporal change patterns of laboratory data may provide insightful clues into the whole course of COVID-19. This study aimed to evaluate longitudinal change patterns of key...     

Serologic Response to SARS-CoV-2 in COVID-19 Patients with Different Severity

Virologica Sinica - The immense patient number caused by coronavirus disease 2019 (COVID-19) global pandemic brings the urge for more knowledge about its immunological features, including the...     

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.     

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.     

Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales

The familial placements of Cyrtandromoea Zoll. and Wightia Wall., two small and enigmatic South‐East Asian genera, have long been controversial in Lamiales. Here we adopt a two‐step approach to resolve their phylogenetic relationships. We initially reconstructed a large‐scale phylogeny of Lamiales using six chloroplast markers (atpB, matK, ndhF, psbBTNH, rbcL, and rps4). The results showed that both Cyrtandromoea and Wightia emerged in the LMPO clade, including Lamiaceae, Mazaceae, Phrymaceae, Paulowniaceae, and Orobanchaceae. Based on the second set of six chloroplast markers (atpB, matK, ndhF, rbcL, rps16, and trnL‐F) and two nuclear ribosomal regions (external transcribed spacer and internal transcribed spacer) for the analyses focusing on the LMPO clade, our results revealed that Cyrtandromoea was consistently nested within Phrymaceae, whereas Wightia was supported as sister to Phrymaceae by the chloroplast DNA dataset or sister to Paulowniaceae by the nuclear ribosomal DNA dataset. Morphological and anatomical evidence fully supports the inclusion of Cyrtandromoea in Phrymaceae, and an updated tribal classification is done for Phrymaceae with five tribes, that is, Cyrtandromoeeae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Diplaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Leucocarpeae, Mimuleae, and Phrymeae. The conflicting phylogenetic position of Wightia indicated by different genome markers results in difficulty placing the genus in either Phrymaceae or Paulowniaceae. Considering the distinct morphological differences between Wightia and other families in the LMPO clade, we here propose a new family, Wightiaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, fam. nov., to accommodate it, which is the 26th family recognized in Lamiales.     

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.     

RHCG基因在非小细胞肺癌中的表达及对细胞增殖的影响

为了探讨Rh type C glycoprotein (RHCG)对非小细胞肺癌(non-small cell lung cancer,NSCLC)细胞增殖的影响及可能的作用机制,本研究使用荧光定量PCR法检测12对NSCLC及癌旁组织样本中RHCG mRNA的表达水平及pcDNA3.1-RHCG质粒对A549细胞RHCG m RNA的表达;采用CCK-8法检测细胞增殖能力;运用PI染色法检测细胞周期;使用免疫印迹法检p-PI3K、PI3K、p-AKT以及AKT蛋白表达水平。本研究发现,与癌旁组织比较,NSCLC中RHCG m RNA表达水平明显降低。RHCG过表达能抑制NSCLC细胞系A549细胞增殖能力。此外,RHCG过表达使A549细胞周期G1/S期转化发生阻滞。本研究还发现,RHCG过表达可下调A549细胞p-PI3K/PI3K和p-AKT/AKT水平。本研究表明,RHCG抑制NSCLC细胞增殖的作用与其抑制PI3K/AKT信号通路有关。