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.     

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.     

Activation of the bitter taste sensor TRPM5 prevents high salt-induced cardiovascular dysfunction

Science China Life Sciences - High salt intake is a known risk factor of cardiovascular diseases. Our recent study demonstrated that long-term high salt intake impairs transient receptor potential...     

Polymorphism analysis and supertype definition of swine leukocyte antigen class I molecules in three-way crossbred (Landrace,Duroc, and Yorkshire) pigs: implications for the vaccine development of African swine fever virus

正Dear Editor,Swine major histocompatibility complex (MHC) is a highly polymorphic gene in pigs and is also called swine leukocyte antigen (SLA)(Fan et al., 2018). SLA is divided into three major categories, SLA Ⅰ (SLA-1,-2,-3), SLA Ⅱ, and SLA Ⅲ(Smith et al., 2005). SLA Ⅰ plays an important role in cellular immunity which can eliminate viruses and other foreign     

无花果果皮中花青素的提取工艺的建立

本研究使用单因素方法考察了无花果(Ficus carica L.)果皮中花青素的最佳提取条件,并考察了7种参数对花青素提取率的影响。参数设置如下:溶剂性质(水,甲醇,乙醇和丙酮)、提取次数(1~3次)、固液比(1/50,1/100,1/150和1/200)、提取时间(60 min,120 min,180 min和240 min)、甲醇浓度(0,20%,40%,60%,80%和100%)、酸类型(盐酸,乙酸,柠檬酸和酒石酸)和酸浓度(0,1%,2%,5%和10%)。使用pH-示差法测量无花果果皮中单体花色素的含量。研究显示,无花果果皮中花青素的最佳提取条件为:溶剂为甲醇溶剂,提取次数为2次,固液比为1/100,提取时间为180 min,甲醇浓度为80%,酸类型为柠檬酸,柠檬酸浓度为5%。该最佳提取条件下的花青素的提取率达到最高(345.62 mg/100g DS)。     

Exogenous maltose enhances Zebrafish immunity to levofloxacin-resistant Vibrio alginolyticus

Understanding the interplay between bacterial fitness, antibiotic resistance, host immunity and host metabolism could guide treatment and improve immunity against antibiotic-resistant pathogens. The acquisition of levofloxacin (Lev) resistance affects the fitness of Vibrio alginolyticus in vitro and in vivo. Lev-resistant (Lev-R) V. alginolyticus exhibits slow growth, reduced pathogenicity and greater resistance to killing by the host, Danio rerio (zebrafish), than Lev-sensitive (Lev-S) V. alginolyticus, suggesting that Lev-R V. alginolyticus triggers a weaker innate immune response in D. rerio than Lev-S V. alginolyticus. Differences were detected in the metabolome of D. rerio infected with Lev-S or Lev-R V. alginolyticus. Maltose, a crucial metabolite, is significantly downregulated in D. rerio infected with Lev-R V. alginolyticus, and exogenous maltose enhances the immune response of D. rerio to Lev-R V. alginolyticus, leading to better clearance of the infection. Furthermore, we demonstrate that exogenous maltose stimulates the host production of lysozyme and its binding to Lev-R V. alginolyticus, which depends on bacterial membrane potential. We suggest that exogenous exposure to crucial metabolites could be an effective strategy for treating and/or managing infections with antibiotic-resistant bacteria.