Xiu-Fang Ou, Ying Wu, Ning Li, Li-Li Jiang, Bao Liu, Lei Gong
The integration of science and education is an effective way for universities to cultivate students in cutting-edge innovative interests. Epigenetics is the expansion of classical genetics, the corresponding experimental courses of which have not been integrated into the current teaching system. In this paper, by taking advantage of our laboratory's research on the DNA methylation maintenance gene, OsMET1-2 in rice, we have integrated our innovative findings in the education curriculum, and built a comprehensive teaching system on experimentation research, which greatly stimulates the curiosity of the students. Taking the OsMET1-2 mutants and its isogenic wild-type rice plants as experimental materials, this course has successfully demonstrated a causal link between genetic mutation and epigenetic variation, a topic widely interested by the students in learning genetics and epigenetics. Through the practice of this course, students have a deeper understanding of the important role of epigenetic modifications, their scientific research capabilities have been greatly improved, thereby strongly supporting the cultivation of top innovative talents among the students.
{"title":"Epigenetics comprehensive experimental course based on the integration of science and education to cultivate students' ability of cutting-edge innovation.","authors":"Xiu-Fang Ou, Ying Wu, Ning Li, Li-Li Jiang, Bao Liu, Lei Gong","doi":"10.16288/j.yczz.23-179","DOIUrl":"10.16288/j.yczz.23-179","url":null,"abstract":"<p><p>The integration of science and education is an effective way for universities to cultivate students in cutting-edge innovative interests. Epigenetics is the expansion of classical genetics, the corresponding experimental courses of which have not been integrated into the current teaching system. In this paper, by taking advantage of our laboratory's research on the DNA methylation maintenance gene, OsMET1-2 in rice, we have integrated our innovative findings in the education curriculum, and built a comprehensive teaching system on experimentation research, which greatly stimulates the curiosity of the students. Taking the OsMET1-2 mutants and its isogenic wild-type rice plants as experimental materials, this course has successfully demonstrated a causal link between genetic mutation and epigenetic variation, a topic widely interested by the students in learning genetics and epigenetics. Through the practice of this course, students have a deeper understanding of the important role of epigenetic modifications, their scientific research capabilities have been greatly improved, thereby strongly supporting the cultivation of top innovative talents among the students.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 12","pages":"1158-1168"},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wen-Zhen Du, Yuan-Jing Li, Jia-Ling Wu, Si-Yu Chen, Liang Jiang, Gang Liu, Ning Xie
The lytic polysaccharide monooxygenase (LPMO) in the auxiliary active protein family (AA family) catalyzes the oxidative depolymerization of various refractory carbohydrates including cellulose, chitin and starch. While accumulating studies investigate the enzymology of LPMO, the research on the inactivation of LPMO genes has been rarely explored. In this study, five LPMO genes PaLPMO11A (Pa_4_4790), PaLPMO11B (Pa_1_5310), PaLPMO11C (Pa_2_7840), PaLPMO11D (Pa_2_8610) and PaLPMO11E (Pa_3_9420) of the AA11 family in the filamentous fungus Podospora anserina were knocked out by homologous recombination. Single mutants ΔPaLPMO11A (ΔA), ΔPaLPMO11B (ΔB), ΔPaLPMO11C (ΔC), ΔPaLPMO11D (ΔD) and ΔPaLPMO11E (ΔE) were constructed, and then all polygenic mutants were constructed via genetic crosses. The differences in the growth rate and sexual reproduction between wild type and mutant strains were observed on different carbon source media. The alteration of oxidative stress and cellulose degradation ability were found on DAB and NBT staining and cellulase activity determination. These results implicated that LPMO11 genes play a key role in the growth, development, and lignocellulose degradation of P. anserina. The results showed that the spore germination efficiency, growth rate and reproductive capacity of mutant strains including ΔBΔCΔE, ΔAΔBΔCΔE, ΔAΔCΔDΔE and ΔAΔBΔCΔDΔE was significantly decreased on different cellulose carbon sources and the remaining strains have no difference. The reduced utilization of various carbon sources, the growth rate, the spore germination rate, the number of fruiting bodies, the normal fruiting bodies, the shortened life span and the ability to degrade cellulose were found in strains which all five genes in the PaLPMO11 family were deleted. However, the strain still had 45% cellulase activity compared to wild type. These results suggest that LPMO11 genes may be involved in the growth and development, sexual reproduction, senescence and cellulose degradation of P. anserina. This study provides information for systematically elucidating the regulatory mechanism of lignocellulose degradation in filamentous fungus P. anserina.
辅助活性蛋白家族(AA 家族)中的溶多糖单加氧酶(LPMO)可催化纤维素、几丁质和淀粉等多种难溶性碳水化合物的氧化解聚。虽然对 LPMO 的酶学研究不断增加,但对 LPMO 基因失活的研究却很少。本研究通过同源重组敲除了丝状真菌Podospora anserina中AA11家族的5个LPMO基因PaLPMO11A(Pa_4_4790)、PaLPMO11B(Pa_1_5310)、PaLPMO11C(Pa_2_7840)、PaLPMO11D(Pa_2_8610)和PaLPMO11E(Pa_3_9420)。构建了单突变体ΔPaLPMO11A(ΔA)、ΔPaLPMO11B(ΔB)、ΔPaLPMO11C(ΔC)、ΔPaLPMO11D(ΔD)和ΔPaLPMO11E(ΔE),然后通过遗传杂交构建了所有多基因突变体。在不同碳源培养基上,观察到野生型和突变株在生长速度和有性生殖方面的差异。通过 DAB 和 NBT 染色以及纤维素酶活性测定,发现了氧化应激和纤维素降解能力的变化。这些结果表明,LPMO11 基因在 P. anserina 的生长、发育和木质纤维素降解过程中起着关键作用。结果表明,ΔBΔCΔE、ΔAΔBΔCΔE、ΔAΔCΔDΔE和ΔAΔBΔCΔDΔE等突变株对不同纤维素碳源的孢子萌发效率、生长速率和繁殖能力均显著下降,其余株系无差异。删除了 PaLPMO11 家族全部五个基因的菌株对各种碳源的利用率、生长速度、孢子萌发率、子实体数量、正常子实体、寿命缩短以及降解纤维素的能力都有所下降。然而,与野生型相比,该菌株仍具有 45% 的纤维素酶活性。这些结果表明,LPMO11 基因可能参与了 P. anserina 的生长发育、有性生殖、衰老和纤维素降解。本研究为系统阐明丝状真菌 P. anserina 降解木质纤维素的调控机制提供了信息。
{"title":"Identification and functional study of AA11 family polysaccharide monooxygenase genes in filamentous fungus Podospora anserina.","authors":"Wen-Zhen Du, Yuan-Jing Li, Jia-Ling Wu, Si-Yu Chen, Liang Jiang, Gang Liu, Ning Xie","doi":"10.16288/j.yczz.23-223","DOIUrl":"10.16288/j.yczz.23-223","url":null,"abstract":"<p><p>The lytic polysaccharide monooxygenase (LPMO) in the auxiliary active protein family (AA family) catalyzes the oxidative depolymerization of various refractory carbohydrates including cellulose, chitin and starch. While accumulating studies investigate the enzymology of LPMO, the research on the inactivation of LPMO genes has been rarely explored. In this study, five LPMO genes PaLPMO11A (Pa_4_4790), PaLPMO11B (Pa_1_5310), PaLPMO11C (Pa_2_7840), PaLPMO11D (Pa_2_8610) and PaLPMO11E (Pa_3_9420) of the AA11 family in the filamentous fungus Podospora anserina were knocked out by homologous recombination. Single mutants ΔPaLPMO11A (ΔA), ΔPaLPMO11B (ΔB), ΔPaLPMO11C (ΔC), ΔPaLPMO11D (ΔD) and ΔPaLPMO11E (ΔE) were constructed, and then all polygenic mutants were constructed via genetic crosses. The differences in the growth rate and sexual reproduction between wild type and mutant strains were observed on different carbon source media. The alteration of oxidative stress and cellulose degradation ability were found on DAB and NBT staining and cellulase activity determination. These results implicated that LPMO11 genes play a key role in the growth, development, and lignocellulose degradation of P. anserina. The results showed that the spore germination efficiency, growth rate and reproductive capacity of mutant strains including ΔBΔCΔE, ΔAΔBΔCΔE, ΔAΔCΔDΔE and ΔAΔBΔCΔDΔE was significantly decreased on different cellulose carbon sources and the remaining strains have no difference. The reduced utilization of various carbon sources, the growth rate, the spore germination rate, the number of fruiting bodies, the normal fruiting bodies, the shortened life span and the ability to degrade cellulose were found in strains which all five genes in the PaLPMO11 family were deleted. However, the strain still had 45% cellulase activity compared to wild type. These results suggest that LPMO11 genes may be involved in the growth and development, sexual reproduction, senescence and cellulose degradation of P. anserina. This study provides information for systematically elucidating the regulatory mechanism of lignocellulose degradation in filamentous fungus P. anserina.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 12","pages":"1128-1146"},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
To compare and analyze the molecular mechanisms of adipose deposition in subcutaneous fat (SAF)and intramuscular fat (IMF) tissues in Ningxiang pigs, differential gene expression profiles in SAF and IMF tissues of Ningxiang pigs were identified and analysed using RNA-seq technology. Six healthy 250-day-old male Ningxiang pigs with similar body weights (approximately 85 kg) of intraspecific individuals were selected as experimental material and samples of SAF and IMF tissues were collected. Differential genes associated with fat deposition and lipid metabolism were obtained by sequencing two adipose tissue transcriptomes and performing GO (Gene Ontology) functional annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis. To verify the reliability of the sequencing results, six differential genes were randomly selected to validate using qRT-PCR. The results showed that we identified 2406 DEGs, with 1422 up-regulated and 984 down-regulated genes in two tissues. GO functional annotation analysis revealed that the differentially expressed genes were mainly involved in lipid metabolism related pathways, such as steroid biosynthesis, unsaturated fatty acid biosynthesis, glycerophospholipid metabolism and autophagy pathway. KEGG pathway enrichment showed that the differentially expressed genes were mainly enriched in the biological processes related to lipid binding, fatty acid metabolism, glycol ester metabolism, lipid biosynthesis and other biological processes related to lipid metabolism. Genes related to lipid metabolism, such as TCAP, NR4A1, ACACA, LPL, ELOVL6, DGAT1, PRKAA1, ATG101, TP53INP2, FDFT1, ACOX1 and SCD were identified by bioinformatic analyses and verified by qRT-PCR. Our results indicated that these genes may play important roles in the regulation of fat deposition and metabolism in the SAF and IMF tissue, providing the further mechanistic investigation of fat deposition in Ningxiang pigs.
为了比较和分析宁乡猪皮下脂肪(SAF)和肌内脂肪(IMF)组织脂肪沉积的分子机制,利用RNA-seq技术鉴定和分析了宁乡猪SAF和IMF组织的差异基因表达谱。实验选取 6 头 250 日龄、体重相近(约 85 千克)的健康雄性宁乡猪作为实验材料,采集其 SAF 和 IMF 组织样本。通过对两个脂肪组织转录组测序,并进行GO(基因本体)功能注释和KEGG(京都基因和基因组百科全书)通路富集分析,获得了与脂肪沉积和脂质代谢相关的差异基因。为了验证测序结果的可靠性,我们随机选择了六个差异基因,使用 qRT-PCR 进行验证。结果显示,我们在两个组织中发现了2406个DEGs,其中上调基因1422个,下调基因984个。GO功能注释分析显示,差异表达基因主要涉及脂质代谢相关通路,如类固醇生物合成、不饱和脂肪酸生物合成、甘油磷脂代谢和自噬通路。KEGG 通路富集显示,差异表达基因主要富集在脂质结合、脂肪酸代谢、乙二醇酯代谢、脂质生物合成等与脂质代谢相关的生物过程中。通过生物信息学分析确定了与脂质代谢相关的基因,如 TCAP、NR4A1、ACACA、LPL、ELOVL6、DGAT1、PRKAA1、ATG101、TP53INP2、FDFT1、ACOX1 和 SCD,并通过 qRT-PCR 进行了验证。结果表明,这些基因可能在调控SAF和IMF组织的脂肪沉积和代谢中发挥重要作用,为进一步研究宁乡猪的脂肪沉积机理提供了依据。
{"title":"Analysis of transcriptome differences between subcutaneous and intramuscular adipose tissue of Ningxiang pigs.","authors":"Fang Wang, Yue-Bo Zhang, Qian Jiang, Yu-Long Yin, Bi-E Tan, Jia-Shun Chen","doi":"10.16288/j.yczz.23-131","DOIUrl":"10.16288/j.yczz.23-131","url":null,"abstract":"<p><p>To compare and analyze the molecular mechanisms of adipose deposition in subcutaneous fat (SAF)and intramuscular fat (IMF) tissues in Ningxiang pigs, differential gene expression profiles in SAF and IMF tissues of Ningxiang pigs were identified and analysed using RNA-seq technology. Six healthy 250-day-old male Ningxiang pigs with similar body weights (approximately 85 kg) of intraspecific individuals were selected as experimental material and samples of SAF and IMF tissues were collected. Differential genes associated with fat deposition and lipid metabolism were obtained by sequencing two adipose tissue transcriptomes and performing GO (Gene Ontology) functional annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis. To verify the reliability of the sequencing results, six differential genes were randomly selected to validate using qRT-PCR. The results showed that we identified 2406 DEGs, with 1422 up-regulated and 984 down-regulated genes in two tissues. GO functional annotation analysis revealed that the differentially expressed genes were mainly involved in lipid metabolism related pathways, such as steroid biosynthesis, unsaturated fatty acid biosynthesis, glycerophospholipid metabolism and autophagy pathway. KEGG pathway enrichment showed that the differentially expressed genes were mainly enriched in the biological processes related to lipid binding, fatty acid metabolism, glycol ester metabolism, lipid biosynthesis and other biological processes related to lipid metabolism. Genes related to lipid metabolism, such as TCAP, NR4A1, ACACA, LPL, ELOVL6, DGAT1, PRKAA1, ATG101, TP53INP2, FDFT1, ACOX1 and SCD were identified by bioinformatic analyses and verified by qRT-PCR. Our results indicated that these genes may play important roles in the regulation of fat deposition and metabolism in the SAF and IMF tissue, providing the further mechanistic investigation of fat deposition in Ningxiang pigs.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 12","pages":"1147-1157"},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mycobacterium infection can affect the host's immune function by secreting extracellular effector proteins. ESX (or type VII) system plays an important role in the secretion of effector proteins. ESX system is the protein export system in mycobacteria and many actinomycetes. However, how ESX system secretes and underlying mechanism of action remain unclear. In this review, we introduce the components, function, classification of ESX system and the process of substrates transfer to the peripheral space via this system, and discuss the roles of ESX system in antibiotics resistance, persistence, host-phage interaction, new drug targets. We hope to provide insights into the discovery of new drugs and vaccine antigens for tuberculosis.
分枝杆菌感染可通过分泌细胞外效应蛋白影响宿主的免疫功能。ESX(或 VII 型)系统在分泌效应蛋白方面发挥着重要作用。ESX 系统是分枝杆菌和许多放线菌的蛋白质输出系统。然而,ESX 系统如何分泌及其作用机制仍不清楚。在这篇综述中,我们将介绍 ESX 系统的组成、功能、分类以及底物通过该系统转移到外周空间的过程,并讨论 ESX 系统在抗生素耐药性、持久性、宿主与噬菌体相互作用、新药靶点等方面的作用。我们希望能为结核病新药和疫苗抗原的发现提供启示。
{"title":"Progress on the function of Mycobacterium T7SS (ESX) secretion system.","authors":"Zhi-Yong Jiang, Jian-Ping Xie","doi":"10.16288/j.yczz.23-188","DOIUrl":"10.16288/j.yczz.23-188","url":null,"abstract":"<p><p>Mycobacterium infection can affect the host's immune function by secreting extracellular effector proteins. ESX (or type VII) system plays an important role in the secretion of effector proteins. ESX system is the protein export system in mycobacteria and many actinomycetes. However, how ESX system secretes and underlying mechanism of action remain unclear. In this review, we introduce the components, function, classification of ESX system and the process of substrates transfer to the peripheral space via this system, and discuss the roles of ESX system in antibiotics resistance, persistence, host-phage interaction, new drug targets. We hope to provide insights into the discovery of new drugs and vaccine antigens for tuberculosis.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 12","pages":"1100-1113"},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Normal oogenesis is crucial to successful reproduction. During the human female fetal stage, primordial germ cells transform from mitosis to meiosis. After synapsis and recombination of homologous chromosomes, meiosis is arrested at the diplotene stage of prophase in meiosis I. The maintenance of oocyte meiotic arrest in the follicle is primarily attributed to high cytoplasmic concentrations of cyclic adenosine monophosphate. During the menstrual cycle, follicle-stimulating hormone and luteinizing hormone lead to the resumption of meiosis that occurs in certain oocytes and complete the ovulation process. Anything that disturbs oocyte meiosis may result in failure of oogenesis and seriously affect both the fertilization and embryonic development. The rapid development of the assisted reproduction technology, high-throughput sequencing technology, and molecular biology technology provide new ideas and means for human to understand molecular mechanism of meiosis and diagnosis and treatment of oocyte maturation defects. In this review, we mainly summarize the recent physiological and pathological mechanisms of oogenesis, involving homologous recombination, meiotic arrest and resumption, maternal mRNA degradation, post-translational regulation, zona pellucida assembly, and so on. We wish to take this opportunity to raise the awareness of researchers in related fields on oocyte meiosis, providing a theoretical basis for further research and disease treatments.
{"title":"Physiological and pathological mechanisms of oocyte meiosis.","authors":"Zhou Zhou, Qing Sang, Lei Wang","doi":"10.16288/j.yczz.23-170","DOIUrl":"10.16288/j.yczz.23-170","url":null,"abstract":"<p><p>Normal oogenesis is crucial to successful reproduction. During the human female fetal stage, primordial germ cells transform from mitosis to meiosis. After synapsis and recombination of homologous chromosomes, meiosis is arrested at the diplotene stage of prophase in meiosis I. The maintenance of oocyte meiotic arrest in the follicle is primarily attributed to high cytoplasmic concentrations of cyclic adenosine monophosphate. During the menstrual cycle, follicle-stimulating hormone and luteinizing hormone lead to the resumption of meiosis that occurs in certain oocytes and complete the ovulation process. Anything that disturbs oocyte meiosis may result in failure of oogenesis and seriously affect both the fertilization and embryonic development. The rapid development of the assisted reproduction technology, high-throughput sequencing technology, and molecular biology technology provide new ideas and means for human to understand molecular mechanism of meiosis and diagnosis and treatment of oocyte maturation defects. In this review, we mainly summarize the recent physiological and pathological mechanisms of oogenesis, involving homologous recombination, meiotic arrest and resumption, maternal mRNA degradation, post-translational regulation, zona pellucida assembly, and so on. We wish to take this opportunity to raise the awareness of researchers in related fields on oocyte meiosis, providing a theoretical basis for further research and disease treatments.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 12","pages":"1087-1099"},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene chip is a high-throughput technique for detecting specific DNA sequences by DNA or DNA-RNA complementary hybridization, among which SNP genotyping chips have been widely employed in the animal genetics and breeding, and have made great achievements in cattle (Bos taurus), pigs (Sus scrofa), sheep (Caprinae), chickens (Gallus gallus) and other livestock. However, genomic selection applied in production merely uses genomic information and cannot fully explain the molecular mechanism of complex traits genetics, which limits the accuracy of genomic selection. With the continuous progresses in epigenetic research, the development of commercial methylation chips and the application of the epigenome-wide association study (EWAS), DNA methylation has been extensively used to draw the causal connections between genetics and phenotypes. In the future, it is hopefully expected to develop methylation chips customized for livestock and poultry and explore methylation sites significantly related to economic traits of livestock and poultry through EWAS thereby extending the understanding of causal variation of complex traits. Combining methylation chips and SNP chips, we can capture the epigenomic and genomic information of livestock and poultry, interpret genetic variation more precisely, improve the accuracy of genome selection, and promote the fine evolution of molecular genetic breeding of livestock and poultry. In this review, we summarize the application of SNP chips and depict the prospects of the application of methylation chips in livestock and poultry. This review will provide valuable insights for further application of gene chips in farm animal breeding.
基因芯片是一种通过DNA或DNA-RNA互补杂交检测特定DNA序列的高通量技术,其中SNP基因分型芯片已在动物遗传育种中得到广泛应用,并在牛(Bos taurus)、猪(Sus scrofa)、羊(Caprinae)、鸡(Gallus gallus)等家畜中取得了巨大成就。然而,在生产中应用的基因组选择只是利用基因组信息,不能完全解释复杂性状遗传的分子机理,限制了基因组选择的准确性。随着表观遗传学研究的不断进步、商业甲基化芯片的开发以及全表观基因组关联研究(EWAS)的应用,DNA 甲基化已被广泛用于解释遗传与表型之间的因果关系。未来,有望开发出为畜禽定制的甲基化芯片,并通过 EWAS 探索与畜禽经济性状显著相关的甲基化位点,从而扩展对复杂性状因果变异的认识。结合甲基化芯片和 SNP 芯片,我们可以捕捉畜禽的表观基因组和基因组信息,更精确地解读遗传变异,提高基因组选择的准确性,促进畜禽分子遗传育种的精细化进化。在这篇综述中,我们总结了 SNP 芯片的应用,并描绘了甲基化芯片在畜禽中的应用前景。本综述将为基因芯片在农场动物育种中的进一步应用提供有价值的见解。
{"title":"Application and prospect of gene chip in genetic breeding of livestock and poultry.","authors":"Jia-Hao Wang, Qing-Yao Zhao, Yue-Ling Zhou, Liang-Yu Shi, Chu-Duan Wang, Ying Yu","doi":"10.16288/j.yczz.23-233","DOIUrl":"10.16288/j.yczz.23-233","url":null,"abstract":"<p><p>Gene chip is a high-throughput technique for detecting specific DNA sequences by DNA or DNA-RNA complementary hybridization, among which SNP genotyping chips have been widely employed in the animal genetics and breeding, and have made great achievements in cattle (Bos taurus), pigs (Sus scrofa), sheep (Caprinae), chickens (Gallus gallus) and other livestock. However, genomic selection applied in production merely uses genomic information and cannot fully explain the molecular mechanism of complex traits genetics, which limits the accuracy of genomic selection. With the continuous progresses in epigenetic research, the development of commercial methylation chips and the application of the epigenome-wide association study (EWAS), DNA methylation has been extensively used to draw the causal connections between genetics and phenotypes. In the future, it is hopefully expected to develop methylation chips customized for livestock and poultry and explore methylation sites significantly related to economic traits of livestock and poultry through EWAS thereby extending the understanding of causal variation of complex traits. Combining methylation chips and SNP chips, we can capture the epigenomic and genomic information of livestock and poultry, interpret genetic variation more precisely, improve the accuracy of genome selection, and promote the fine evolution of molecular genetic breeding of livestock and poultry. In this review, we summarize the application of SNP chips and depict the prospects of the application of methylation chips in livestock and poultry. This review will provide valuable insights for further application of gene chips in farm animal breeding.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 12","pages":"1114-1127"},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Invasive infection caused by hypervirulent Klebsiella pneumoniae (HvKP) has been reported worldwide. Most of the patients are community population, related to diabetes mellitus (DM), chronic liver disease and other basic diseases, which prone to systemic migratory infection. In this study, we collected 377 patients with community acquired Klebsiella pneumoniae liver abscess in our hospital from January 2013 to December 2018, 65.8% of whom were male, and 49.6% had DM. Patients with DM are prone to eye and central nervous system (CNS) infection, which need continuous local abscess drainage during treatment. Among them, patients with poor blood glucose control have a higher rate of blood stream infections (BSI). 219 strains of HvKP were obtained, with K1/K2 Serotype accounted for 81.7%. The incidence of BSI in K2 patients was higher than that in K1 patients. The PCR results indicate that the carrying rate of virulence genes (rmpA、areo、kfu、allS、iroN、magA、uge、wcaG) in K1/K2 type strains is significantly higher than that in non K1/K2 type strains. ST23 and ST65 are the most common multilocus sequence typing (MLST), which belong to K1 and K2 Serotype respectively. All of HvKP strains showed high sensitivity to commonly used clinical antibiotics other than ampicillin, with 54.3% of the strains exhibiting high viscosity characteristics. Meanwhile, 35 classic Klebsiella pneumoniae (cKP) strains were collected, and their serum typing is mainly non K1/K2. The carrying rate of virulence genes and viscosity degree in HvKP are significantly higher than those in cKP. Primary liver abscess caused by HvKP is prone to multiple tissue and organ infections, but it shows higher sensitivity to most commonly used antibiotics in clinical practice except for ampicillin. After effective treatment, the overall prognosis of patients is better. This study analyzes the pathogenic characteristics of HvKP and elaborates on the clinical characteristics of patients, which can provide reference for clinical and scientific research work.
{"title":"Comparison of clinical and microbiological characteristics of community-acquired hypervirulent Klebsiella pneumoniae liver abscess in diabetic and non-diabetic patients.","authors":"Jing Ye, Yuan Wang, Lu-Ying Xiong, Yong-Hong Xiao","doi":"10.16288/j.yczz.23-167","DOIUrl":"10.16288/j.yczz.23-167","url":null,"abstract":"<p><p>Invasive infection caused by hypervirulent Klebsiella pneumoniae (HvKP) has been reported worldwide. Most of the patients are community population, related to diabetes mellitus (DM), chronic liver disease and other basic diseases, which prone to systemic migratory infection. In this study, we collected 377 patients with community acquired Klebsiella pneumoniae liver abscess in our hospital from January 2013 to December 2018, 65.8% of whom were male, and 49.6% had DM. Patients with DM are prone to eye and central nervous system (CNS) infection, which need continuous local abscess drainage during treatment. Among them, patients with poor blood glucose control have a higher rate of blood stream infections (BSI). 219 strains of HvKP were obtained, with K1/K2 Serotype accounted for 81.7%. The incidence of BSI in K2 patients was higher than that in K1 patients. The PCR results indicate that the carrying rate of virulence genes (rmpA、areo、kfu、allS、iroN、magA、uge、wcaG) in K1/K2 type strains is significantly higher than that in non K1/K2 type strains. ST23 and ST65 are the most common multilocus sequence typing (MLST), which belong to K1 and K2 Serotype respectively. All of HvKP strains showed high sensitivity to commonly used clinical antibiotics other than ampicillin, with 54.3% of the strains exhibiting high viscosity characteristics. Meanwhile, 35 classic Klebsiella pneumoniae (cKP) strains were collected, and their serum typing is mainly non K1/K2. The carrying rate of virulence genes and viscosity degree in HvKP are significantly higher than those in cKP. Primary liver abscess caused by HvKP is prone to multiple tissue and organ infections, but it shows higher sensitivity to most commonly used antibiotics in clinical practice except for ampicillin. After effective treatment, the overall prognosis of patients is better. This study analyzes the pathogenic characteristics of HvKP and elaborates on the clinical characteristics of patients, which can provide reference for clinical and scientific research work.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 11","pages":"1052-1061"},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Guanylate-binding proteins (GBPs) are a subfamily of interferon-inducible proteins that undertake distinct roles in the the context of bacteria, virus, chlamydia and parasites infections. These proteins exert a notable influence on the progression and outcomes of infectious diseases. Within the realm of host cell-autonomous immunity against pathogens, GBPs have been identified as the regulators of pyroptosis through canonical and noncanonical inflammasome activation pathways. In this review, we summarize the structure and evolution of GBP family members, the canonical and noncanonical inflammasome activation pathways, the roles of GBPs in regulating inflammasome activation, and the mechanisms of GBPs affecting infections induced by different pathogens. We hope to provide new basic research clues for the pathogenesis and diagnosis and treatment of infectious diseases.
{"title":"Advances in the regulation of inflammasome activation by GBP family in infectious diseases.","authors":"Shu-Ting Quan, Wei-Wei Jiao, Fang Xu, Lin Sun, Hui Qi, Adong Shen","doi":"10.16288/j.yczz.23-119","DOIUrl":"10.16288/j.yczz.23-119","url":null,"abstract":"<p><p>Guanylate-binding proteins (GBPs) are a subfamily of interferon-inducible proteins that undertake distinct roles in the the context of bacteria, virus, chlamydia and parasites infections. These proteins exert a notable influence on the progression and outcomes of infectious diseases. Within the realm of host cell-autonomous immunity against pathogens, GBPs have been identified as the regulators of pyroptosis through canonical and noncanonical inflammasome activation pathways. In this review, we summarize the structure and evolution of GBP family members, the canonical and noncanonical inflammasome activation pathways, the roles of GBPs in regulating inflammasome activation, and the mechanisms of GBPs affecting infections induced by different pathogens. We hope to provide new basic research clues for the pathogenesis and diagnosis and treatment of infectious diseases.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 11","pages":"1007-1017"},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xin Yang, Yong-Xiang Wu, Yu Leng, Jia-Chen Li, Chao-Jie Wang, Yi-Mei Yuan, Zhen Wang, Lan Zhang, Hao Li, Wei Liu
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease, caused by severe fever with thrombocytopenia syndrome virus (SFTSV), which is primarily transmitted via tick bites. Clusters of SFTS caused by human-to-human transmission have been reported both at home and abroad, mainly focused on the transmission or exposure modes. However, the correlation between SFTS clusters and viral genotypes has not been investigated. This study mainly reported two clusters of SFTS in Xinyang City, Henan Province, from 2022 to 2023, discussed the possible route of person-to-person transmission of SFTSV infection and analyzed the association between SFTS clusters and virus genotypes. We found that two groups of SFTSV in two clusters were clustered separately into different genotypes through viral sequence analysis of 4 confirmed patients. We also performed phylogenetic analysis, after including SFTSV sequences obtained from SFTS clusters deposited in the GenBank. Three SFTSV genotypes have been reported among cases of human-to-human transmission, suggesting that the occurrence of SFTS clusters may not be related to SFTSV genotypes. This study provided genetic evidence for revealing the chain of human-to-human transmission of SFTS clusters, indicating that contact with patients' blood is an important transmission route of SFTSV. The findings laid the foundation for preventing and controlling human-to-human transmission of SFTS.
{"title":"Epidemiololgical and etiological analysis of two clusters of severe fever with thrombocytopenia syndrome.","authors":"Xin Yang, Yong-Xiang Wu, Yu Leng, Jia-Chen Li, Chao-Jie Wang, Yi-Mei Yuan, Zhen Wang, Lan Zhang, Hao Li, Wei Liu","doi":"10.16288/j.yczz.23-176","DOIUrl":"10.16288/j.yczz.23-176","url":null,"abstract":"<p><p>Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease, caused by severe fever with thrombocytopenia syndrome virus (SFTSV), which is primarily transmitted via tick bites. Clusters of SFTS caused by human-to-human transmission have been reported both at home and abroad, mainly focused on the transmission or exposure modes. However, the correlation between SFTS clusters and viral genotypes has not been investigated. This study mainly reported two clusters of SFTS in Xinyang City, Henan Province, from 2022 to 2023, discussed the possible route of person-to-person transmission of SFTSV infection and analyzed the association between SFTS clusters and virus genotypes. We found that two groups of SFTSV in two clusters were clustered separately into different genotypes through viral sequence analysis of 4 confirmed patients. We also performed phylogenetic analysis, after including SFTSV sequences obtained from SFTS clusters deposited in the GenBank. Three SFTSV genotypes have been reported among cases of human-to-human transmission, suggesting that the occurrence of SFTS clusters may not be related to SFTSV genotypes. This study provided genetic evidence for revealing the chain of human-to-human transmission of SFTS clusters, indicating that contact with patients' blood is an important transmission route of SFTSV. The findings laid the foundation for preventing and controlling human-to-human transmission of SFTS.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 11","pages":"1062-1073"},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mismatch repair (MMR) is a common repair system after DNA replication, which is critical for maintaining genomic stability. Members of the MutS and MutL protein families are involved in key steps of mismatch repair. Despite the major importance of this repair pathway, MutS-MutL are absent in almost all Actinobacteria and many Archaea. Mycobacteria and others have another non-canonical MMR pathway, in which EndoMS/NucS plays a key role and has no structural homology compared to canonical MMR proteins (MutS/MutL). EndoMS/NucS mediated non-canonical mismatch repair plays an important role in DNA repair, mutation, homologous recombination and antibiotic resistance of Mycobacterium. By comparing the classical and non-canonical MMR pathways, this paper reviews the EndoMS/NucS-mediated non-canonical MMR pathway in Mycobacterium and its recent progress. We hope to bring new insights into the molecular mechanism of mycobacterial mismatch repair as well as to provide new research clues for mycobacterial antibiotic therapy.
错配修复(MMR)是 DNA 复制后的一种常见修复系统,对维持基因组稳定性至关重要。MutS 和 MutL 蛋白家族的成员参与了错配修复的关键步骤。尽管这一修复途径非常重要,但几乎所有放线菌和许多古细菌中都不存在 MutS-MutL。分枝杆菌等有另一种非规范的错配修复途径,其中 EndoMS/NucS 起着关键作用,与规范的错配修复蛋白(MutS/MutL)相比没有结构上的同源性。EndoMS/NucS 介导的非规范错配修复在分枝杆菌的 DNA 修复、突变、同源重组和抗生素耐药性方面发挥着重要作用。本文通过比较经典和非经典MMR途径,回顾了分枝杆菌中EndoMS/NucS介导的非经典MMR途径及其最新进展。希望能对分枝杆菌错配修复的分子机制有新的认识,并为分枝杆菌抗生素治疗提供新的研究线索。
{"title":"Progress on the non-canonical mismatch repair in Mycobacterium and its role in antibiotic resistance.","authors":"Sha-Sha Xiang, Jian-Ping Xie","doi":"10.16288/j.yczz.23-236","DOIUrl":"10.16288/j.yczz.23-236","url":null,"abstract":"<p><p>Mismatch repair (MMR) is a common repair system after DNA replication, which is critical for maintaining genomic stability. Members of the MutS and MutL protein families are involved in key steps of mismatch repair. Despite the major importance of this repair pathway, MutS-MutL are absent in almost all Actinobacteria and many Archaea. Mycobacteria and others have another non-canonical MMR pathway, in which EndoMS/NucS plays a key role and has no structural homology compared to canonical MMR proteins (MutS/MutL). EndoMS/NucS mediated non-canonical mismatch repair plays an important role in DNA repair, mutation, homologous recombination and antibiotic resistance of Mycobacterium. By comparing the classical and non-canonical MMR pathways, this paper reviews the EndoMS/NucS-mediated non-canonical MMR pathway in Mycobacterium and its recent progress. We hope to bring new insights into the molecular mechanism of mycobacterial mismatch repair as well as to provide new research clues for mycobacterial antibiotic therapy.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"45 11","pages":"1018-1027"},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141065682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}