基于高通量测序的麦红吸浆虫转录组分析

麦红吸浆虫Sitodiplosis mosellana(Gehin)是一种世界性的小麦害虫。为获得其转录组信息,本研究采用新一代高通量测序技术Illumina HiSeq TM 2000对麦红吸浆虫成虫转录组进行测序。共获得转录组样本数据量为27.88 G,经分析共获得59257个Unigenes,总长度49861164 bp,最短20 bp,最长29282 bp,平均长度841 bp。将Unigenes序列与NR、NT、Swiss-Prot、KEGG、GO和KOG数据库进行比对(e≤10-10),共获得95029个结果。通过GO功能分类,共有19584个Unigenes在GO数据库中细胞组分、分子功能和生物学过程等3大类50个功能组中找到对应。与KOG数据库进行比对,共有11279个麦红吸浆虫Unigenes被注释,按功能大致可分为26类。通过KEGG pathways分析,共有9110个麦红吸浆虫Unigenes被注释,分别归属于细胞进程、环境信息进程、遗传信息进程、新陈代谢和有机体系统5大类代谢途径,主要包括细胞生长与死亡、细胞运动、信号转导、能量代谢等32类代谢途径。CDS预测发现30088条序列可被编码,占全部基因的50.78%。SSR位点查找发现,在59257个Unigenes中共找到36323个SSR位点,发生率为61.30%。本研究获得的巨大的麦红吸浆虫转录组信息,为麦红吸浆虫的功能基因挖掘提供了重要的信息资源。     

Long-Term Existence of SARS-CoV-2 in COVID-19 Patients: Host Immunity,Viral Virulence,and Transmissibility

Virologica Sinica - COVID-19 patients can recover with a median SARS-CoV-2 clearance of 20 days post initial symptoms (PIS). However, we observed some COVID-19 patients with existing...     

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.     

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     

The structure and antimicrobial potential of wasp and hornet (Vespidae) mastoparans: A review

Wasp venom is a complex mixture of biologically active components, including high molecular weight proteins, small peptides, bioactive amines, and amino acids. Peptides comprise up to 70% of dried venom. In social wasp venoms, three of the major peptide types are mastoparans, which cause mast cell degranulation, chemotactic peptides, which promote chemotaxis of polymorphonucleated leukocytes, and kinin‐related peptides, which are known to produce pain and increase vascular permeability. Among these, the bioactive tridecapeptide mastoparan is the most common and may even have antimicrobial activity. Herein we summarize the results of studies on vespid mastoparans, focusing on hornets (Vespa spp.) identified following a systematic literature search for mastoparans of hornets in the genus Vespa, the most active mastoparan research taxon. The common features of hornet mastoparans are C‐terminal amidation, amphipathic helical structure, and multiple functions such as mast cell degranulation and hemolysis, as well as membrane permeabilization. Most interestingly, all tested hornet mastoparans have strong antimicrobial activities, suggesting that they can provide useful insights into and opportunities for development of novel antibacterial peptides.     

Insect diversity in Gonggeom‐ji,the first protected paddy field wetland in Korea

Gonggeom‐ji pond is the first protected paddy field wetland area, designated by the Ministry of Environment of Korea in 2011, because of its high biodiversity and historic value. It contains reservoirs, paddy fields, and a forest site that provides diverse niches for insects. Quantitative methods were used in this study to estimate the insect diversity of this region. A transect of 50 m was designated in each site (reservoirs, paddy fields, and a forest site). Data were collected using sweeping and pitfall traps along each transect in May, August, and November 2017, representative of the seasons—spring, summer, and autumn, respectively. As a result, a total of 1079 individual insects representing 170 species from 60 families within nine orders were collected. Diversity, richness, and evenness indices were the highest in the forest site in May (4.77, 8.6, and 0.91, respectively). The dominance index was the highest in the forest site in November (0.64). Similarity index was the highest in the reservoir in May and August (0.519). These results would help compare different sites and their vegetation to assess relationships between insects and habitats.     

Protocols for RecET-based markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida

Pseudomonas putida has emerged as a promising host for the production of chemicals and materials thanks to its metabolic versatility and cellular robustness. In particular, P. putida KT2440 has been officially classified as a generally recognized as safe (GRAS) strain, which makes it suitable for the production of compounds that humans directly consume, including secondary metabolites of high importance. Although various tools and strategies have been developed to facilitate metabolic engineering of P. putida, modification of large genes/clusters essential for heterologous expression of natural products with large biosynthetic gene clusters (BGCs) has not been straightforward. Recently, we reported a RecET-based markerless recombineering system for engineering P. putida and demonstrated deletion of multiple regions as large as 101.7 kb throughout the chromosome by single rounds of recombineering. In addition, development of a donor plasmid system allowed successful markerless integration of heterologous BGCs to P. putida chromosome using the recombineering system with examples of – but not limited to – integrating multiple heterologous BGCs as large as 7.4 kb to the chromosome of P. putida KT2440. In response to the increasing interest in our markerless recombineering system, here we provide detailed protocols for markerless gene knockout and integration for the genome engineering of P. putida and related species of high industrial importance.     

Microbial assemblages associated with the rhizosphere and endosphere of an herbage,Leymus chinensis

Root-associated microbiomes play significant roles in plant productivity, health and ecological services. However, our current understanding of the microbial assemblages in the rhizosphere and endosphere of herbage is still limited. To gain insights into these microbial assemblages, Illumina MiSeq high-throughput sequencing was performed to investigate the characteristics of microbial communities of an herbage, Leymus chinensis. Hierarchical clustering analysis and principal coordinate analysis (PCoA) results showed that microbial communities of the rhizosphere and endosphere samples were clearly distinguished. Rhizosphere soil communities showed a greater sensitivity than root endosphere communities using linear discriminant analysis (LDA) effect size (LEfSe). Rhizosphere and endosphere communities performed their respective functions in the soil as a cohesive collective, and Rhizobiales were observed to function as generalists. Redundancy analysis (RDA) and variance partitioning analysis (VPA) results revealed that the contribution of the interaction between soil physicochemical parameters and soil enzymes was greater than their individual contributions. In summary, this study is the first to elucidate the microbial diversity and community structure of L. chinensis and compare the diversity and composition between rhizospheric and endosphere microbiomes.     

An innovative protein expression system using RNA polymerase I for large-scale screening of high-nucleic-acid content Saccharomyces cerevisiae strains

Saccharomyces cerevisiae is the preferred source of RNA derivatives, which are widely used as supplements for foods and pharmaceuticals. As the most abundant RNAs, the ribosomal RNAs (rRNAs) transcribed by RNA polymerase I (Pol I) have no 5′ caps, thus cannot be translated to proteins. To screen high-nucleic-acid content yeasts more efficiently, a cap-independent protein expression system mediated by Pol I has been designed and established to monitor the regulatory changes of rRNA synthesis by observing the variation in the reporter genes expression. The elements including Pol I-recognized rDNA promoter, the internal ribosome entry site from cricket paralytic virus which can recruit ribosomes internally, reporter genes (URA3 and yEGFP3), oligo-dT and an rDNA terminator were ligated to a yeast episomal plasmid. This system based on the URA3 gene worked well by observing the growth phenotype and did not require the disruption of cap-dependent initiation factors. The fluorescence intensity of strains expressing the yEGFP3 gene increased and drifted after mutagenesis. Combined with flow cytometry, cells with higher GFP level were sorted out. A strain showed 58% improvement in RNA content and exhibited no sequence alteration in the whole expression cassette introduced. This study provides a novel strategy for breeding high-nucleic-acid content yeasts.