Parallel Gene Loss and Acquisition Among Strains of Different Brucella Species and Biovars

Zhijun Zhong,Yufei Wang,Jie Xu,Yanfen Chen,Yuehua Ke,Xiaoyan Zhou,Xitong Yuan,Dongsheng Zhou,Yi Yang,Ruifu Yang,Guangneng Peng,Hai Jiang,Jing Yuan,Hongbin Song,Buyun Cui,Liuyu Huang,Zeliang Chen 한국미생물학회 2012 The journal of microbiology Vol.50 No.4

The genus Brucella is divided into six species; of these, B. melitensis and B. abortus are pathogenic to humans, and B. ovis and B. neotomae are nonpathogenic to humans. The definition of gene loss and acquisition is essential for understanding Brucella’s ecology, evolutionary history, and host relationships. A DNA microarray containing unique genes of B. melitensis Type strain 16MT and B. abortus 9-941 was constructed and used to determine the gene contents of the representative strains of Brucella. Phylogenetic relationships were inferred from sequences of housekeeping genes. Gene loss and acquisition of different Brucella species were inferred. A total of 214 genes were found to be differentially distributed,and 173 of them were clustered into 15 genomic islands (GIs). Evidence of horizontal gene transfer was observed for 10GIs. Phylogenetic analysis indicated that the 19 strains formed five clades, and some of the GIs had been lost or acquired independently among the different lineages. The derivation of Brucella lineages is concomitant with the parallel loss or acquisition of GIs, indicating a complex interaction between various Brucella species and hosts.

Effects of turbulent wind and irregular waves on the dynamic characteristics of a floating offshore wind turbine platform

Yinong Tian,Yuguang Zhong,Hengxu Liu,Fankai Kong,Hailong Chen,Zhijun Ma 대한기계학회 2023 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.37 No.6

Studying the dynamic characteristics of the platform under unsteady loads is of great significance to the development of floating offshore wind turbines (FOWTs). In this work, a 15 MW semi-submersible FOWT is extensively simulated using OPENFAST software, and the influence of turbulent wind and irregular waves on the platform‘s motion is analyzed in detail. Results show that the surge motion of the platform of a complete FOWT system is mainly affected by wind speed, and the influence of turbulence intensity (TI) is slightly greater than the wave height. The heave motion is most significantly affected by the wave height. When the wave height is large, the influence of wind speed on the platform gradually decreases, and the effect of TI becomes more evident. The pitch and yaw motions are greatly affected by the wind speed and TI. The research results can serve as a reference for the platform design of large FOWTs in the future.

Temporal expression profiling of long noncoding RNA and mRNA in the peripheral blood during porcine development

Gu, Yiren,Zhou, Rui,Jin, Long,Tao, Xuan,Zhong, Zhijun,Yang, Xuemei,Liang, Yan,Yang, Yuekui,Wang, Yan,Chen, Xiaohui,Gong, Jianjun,He, Zhiping,Li, Mingzhou,Lv, Xuebin Asian Australasian Association of Animal Productio 2020 Animal Bioscience Vol.33 No.5

Objective: We investigated the temporal expression profiles of long noncoding RNA (lncRNA) and mRNA in the peripheral blood of pigs during development and identified the lncRNAs that are related to the blood-based immune system. Methods: Peripheral blood samples were obtained from the pigs at 0, 7, 28, and 180 days and 2 years of age. RNA sequencing was performed to survey the lncRNA and mRNA transcriptomes in the samples. Short time-series expression miner (STEM) was used to show temporal expression patterns in the mRNAs and lncRNAs. Gene ontology and Kyoto encyclopedia of genes and genomes analyses were performed to assess the genes' biological relevance. To predict the functions of the identified lncRNAs, we extracted mRNAs that were nearby loci and highly correlated with the lncRNAs. Results: In total of 5,946 lncRNA and 12,354 mRNA transcripts were identified among the samples. STEM showed that most lncRNAs and mRNAs had similar temporal expression patterns during development, indicating the expressional correlation and functional relatedness between them. The five stages were divided into two classes: the suckling period and the late developmental stage. Most genes were expressed at low level during the suckling period, but at higher level during the late stages. Expression of several T-cell-related genes increased continuously during the suckling period, indicating that these genes are crucial for establishing the adaptive immune system in piglets at this stage. Notably, lncRNA TCONS-00086451 may promote blood-based immune system development by upregulating nuclear factor of activated T-cells cytoplasmic 2 expression. Conclusion: This study provides a catalog of porcine peripheral blood-related lncRNAs and mRNAs and reveals the characteristics and temporal expression profiles of these lncRNAs and mRNAs during peripheral blood development from the newborn to adult stages in pigs.

Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population

Liu, Bin,Shen, Linyuan,Guo, Zhixian,Gan, Mailing,Chen, Ying,Yang, Runling,Niu, Lili,Jiang, Dongmei,Zhong, Zhijun,Li, Xuewei,Zhang, Shunhua,Zhu, Li Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.7

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer

Wei Zhao,Ziwei Ren,Yan Luo,Jianguo Cheng,Jie Wang,Yin Wang,Zexiao Yang,Xueping Yao,Zhijun Zhong,Wei Yang,Xi Wu 한국유전학회 2021 Genes & Genomics Vol.43 No.1

Background The forest musk deer (FMD, Moschus berezovskii) is an threatened species in China. Bacterial pneumonia was found to seriously restrict the development of FMD captive breeding. Historical evidence has demonstrated the relationship between immune system and intestinal Lactobacillus in FMD. Objective We sought to elucidate the diferences in the gut microbiota of healthy and bacterial pneumonia FMD. Methods The bacterial pneumonia FMD was demonstrated by bacterial and pathological diagnosis, and the gut microbiome of healthy and bacterial pneumonia FMD was sequenced and analysed. Results There are three pathogens (Pseudomonas aeruginosa, Streptococcus equinus and Trueperella pyogenes) isolated from the bacterial pneumonia FMD individuals. Compared with the healthy group, the abundance of Firmicutes and Proteobacteria in the pneumonia group was changed, and a high level of Proteobacteria was found in the pneumonia group. In addition, a higher abundance of Acinetobacter (p=0.01) was observed in the population of the pneumonia group compared with the healthy group. Several potentially harmful bacteria and disease-related KEGG subsystems were only found in the gut of the bacterial pneumonia group. Analysis of KEGG revealed that many genes related to type IV secretion system, type IV pilus, lipopolysaccharide export system, HTH-type transcriptional regulator/antitoxin MqsA, and ArsR family transcriptional regulator were signifcantly enriched in the metagenome of the bacterial pneumonia FMD. Conclusion Our results demonstrated that the gut microbiome was signifcantly altered in the bacterial pneumonia group. Overall, our research improves the understanding of the potential role of the gut microbiota in the FMD bacterial pneumonia.