Background Chickens and ducks are vital sources of animal protein for humans.Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species,highlighting the nee...Background Chickens and ducks are vital sources of animal protein for humans.Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species,highlighting the need for more comprehensive genomes.The bird genome has more than tens of microchromosomes,but comparative genomics,annotations,and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies.We aim to complete the chicken and duck genomes,recover missing genes,and reveal common and unique chromosomal features between birds.Results The near telomere-to-telomere genomes of Silkie Gallus gallus and Mallard Anas platyrhynchos were successfully assembled via multiple high-coverage complementary technologies,with quality values of 36.65 and 44.17 for Silkie and Mallard,respectively;and BUSCO scores of 96.55%and 96.97%for Silkie and Mallard,respectively;the mapping rates reached over 99.52%for both assembled genomes,these evaluation results ensured high completeness and accuracy.We successfully annotated 20,253 and 19,621 protein-coding genes for Silkie and Mallard,respectively,and assembled gap-free sex chromosomes in Mallard for the first time.Comparative analysis revealed that microchromosomes differ from macrochromosomes in terms of GC content,repetitive sequence abundance,gene density,and levels of 5mC methylation.Different types of arrangements of centromeric repeat sequence centromeres exist in both Silkie and the Mallard genomes,with Mallard centromeres being invaded by CR1.The highly heterochromatic W chromosome,which serves as a refuge for ERVs,contains disproportionately long ERVs.Both Silkie and the Mallard genomes presented relatively high 5mC methylation levels on sex chromosomes and microchromosomes,and the telomeres and centromeres presented significantly higher 5mC methylation levels than the whole genome.Finally,we recovered 325 missing genes via our new genomes and annotated TNFA in Mallard for the first time,revealing conserved protein structures and tissue-specific expression.Conclusions The near telomere-to-telomere assemblies in Mallard and Silkie,with the first gap-free sex chromosomes in ducks,significantly enhanced our understanding of genetic structures in birds,specifically highlighting the distinctive chromosome features between the chicken and duck genomes.This foundational work also provides a series of newly identified missing genes for further investigation.展开更多
目的:研究CHRNA5亚基突变对尼古丁受体功能的影响。方法:通过RT-PCR克隆CHRNA5基因片段,并通过重叠延伸PCR方法对CHRNA5亚基基因定点突变,从而构建CHRNA5突变型及野生型表达载体,然后转染至HEK293T细胞中,检测其基因表达。并将其分别与C...目的:研究CHRNA5亚基突变对尼古丁受体功能的影响。方法:通过RT-PCR克隆CHRNA5基因片段,并通过重叠延伸PCR方法对CHRNA5亚基基因定点突变,从而构建CHRNA5突变型及野生型表达载体,然后转染至HEK293T细胞中,检测其基因表达。并将其分别与CHRNA3和CHRNB4共转至HEK293T细胞中,检测三质粒共转后的基因表达;通过采用尼古丁持续灌流细胞10 min,然后检测细胞内钙离子内流峰值的变化情况,接下来检测突变对转染后细胞活力的影响。结果:构建的CHRNA5表达载体在转染HEK293T细胞48 h后,能够检测到绿色荧光蛋白的表达,这证明重组载体已成功转染进HEK293T细胞;通过RT-PCR检测出转染细胞CHRNA5 m RNA表达,这证明CHRNA5突变型和野生型均在HEK293T细胞中成功进行了表达。通过尼古丁灌流细胞实验显示突变组和野生型组F340/F380峰值变化均值分别为0.865±0.048和0.447±0.127,突变体组峰值显著高于野生型组(P<0.05)。细胞活力检测实验发现0.01 m M和0.1 m M尼古丁刺激下突变组的细胞活力峰值分别为139%和137%,显著高于野生组的124%和126%,有显著差异(P<0.05)。结论:本研究成功构建了CHRNA5突变及野生型真核表达载体,发现CHRNA5的突变会导致其受体功能性改变,并影响细胞活力。展开更多
Polymerase chain reaction(PCR) was used to amplify 5S rRNA spacer from wild rice(Oryza rufipogon and O.nivara) and cultivated rice(indica and japonica varieties of O.sativa L).The results show that there is spacer len...Polymerase chain reaction(PCR) was used to amplify 5S rRNA spacer from wild rice(Oryza rufipogon and O.nivara) and cultivated rice(indica and japonica varieties of O.sativa L).The results show that there is spacer length variation within and between species,and the typical indica and japonica varieties have their unique banding patterns of amplified 5S rRNA spacers,whereas intermediate showed no specific amplification profile of spacer regions.The 5S rRNA genes in intermediate are either identical with that of indica variety or that of japonica variety.These data suggest that the spacer length polymorphisms can be used to distinguish between closely ralated species and subspecies.展开更多
Summary： This study investigated the effects of benazepril administered in the morning or evening on the diurnal variation of renin-angiotensin-aldosterone system （RAAS） and clock genes in the kidney. The male Wist...Summary： This study investigated the effects of benazepril administered in the morning or evening on the diurnal variation of renin-angiotensin-aldosterone system （RAAS） and clock genes in the kidney. The male Wistar rat models of 5/6 subtotal nephrectomy （STNx） were established. Animals were ran- domly divided into 4 groups： sham STNx group （control）, STNx group, morning benazepril group （MB） and evening benazepril group （EB）. Benazepril was intragastfically administered at a dose of 10 mg/kg/day at 07：00 and 19：00 in the MB group and EB group respectively for 12 weeks. All the animals were synchronized to the light：dark cycle of 12：12 for 12 weeks. Systolic blood pressure （SBP）, 24-h urinary protein excretion and renal function were measured at 11 weeks. Blood samples and kidneys were collected every 4 h throughout a day to detect the expression pattern of renin activity （RA）, angio- tensin Ⅱ （Ang Ⅱ ） and aldosterone （Aid） by radioimmunoassay （RIA） and the mRNA expression profile of clock genes （bmall, dbp and per2） by real-time PCR at 12 weeks. Our results showed that no signifi- cant differences were noted in the SBP, 24-h urine protein excretion and renal function between the MB and EB groups. There were no significant differences in average Aid and RA content of a day between the MB group and EB group. The expression peak of bmall mRNA was phase-delayed by 4 to 8 h, and the diurnal variation of per2 and dbp mRNA diminished in the MB and EB groups compared with the control and STNx groups. It was concluded when the similar SBP reduction, RAAS inhibition and clock gene profile were achieved with optimal dose of benazepril, morning versus evening dosing of benazepril has the same renoprotection effects.展开更多
Reference genes, stably expressing in different tissues and cells, are commonly used as the references in expression analysis. Selecting the optimum reference gene is crucial to the success of experiments. In this stu...Reference genes, stably expressing in different tissues and cells, are commonly used as the references in expression analysis. Selecting the optimum reference gene is crucial to the success of experiments. In this study, the expression stabilities of nine common reference genes, including ACT2, 18 S r RNA, APRT, EF-1α, RNA POL II, TUBα, TUBβ, GAPDH and TLF of Agropyron mongolicum, were studied under drought condition. Among them, 18 S r RNA was found to be the most optimum reference gene under drought stress by the analyzing of ge Norm and Norm Finder software. Quantitative expression levels of P5 CS using 18 S r RNA as the reference gene, and proline contents under drought stress in A. mongolicum were further operated, and we found the expression level of P5 CS gene and proline content had a significantly positive relationship（R^2=0.7763, P〈0.05）. This study established and validated 18 S r RNA as the reference genes in A. mongolicum under drought stress, providing a powerful tool for the quantitative expression analysis of drought genes in A. mongolicum.展开更多
H5N1 influenza represents one of the great challenges to public health.Some H5N1 viruses(i.e.,A/goose/Hubei/65/05,GS/65) are weakly pathogenic,while the others(i.e.,A/duck/Hubei/49/05,DK/49) are highly pathogenic to t...H5N1 influenza represents one of the great challenges to public health.Some H5N1 viruses(i.e.,A/goose/Hubei/65/05,GS/65) are weakly pathogenic,while the others(i.e.,A/duck/Hubei/49/05,DK/49) are highly pathogenic to their natural hosts.Here,we performed brain and spleen transcriptomic analyses of control ducks and ones infected by the DK/49 or the GS/65 H5N1 virus.We demonstrated that,compared to the GS/65 virus,the DK/49 virus infection changed more numerous immune genes’ expression and caused continuous increasing of immune pathways(i.e.,RIG-I and MDA5) in ducks.We found that both H5N1 virus strains might escape or subvert host immune response through affecting alternative translation of immune genes,while the DK/49 virus seemed to induce alternative translation of more immune genes than the GS/65 virus.We also identified five co-expressional modules associated with H5N1 virus replication through the weight correlation network analysis(WGCNA).Moreover,we first demonstrated that the duck BCL2 L15 and DCSTAMP in one of these five modules inhibited both the highly pathogenic and weakly pathogenic H5N1 virus replication efficiently.These analyses,in combination with our comprehensive transcriptomic data,provided global view of the molecular architecture for the interaction between host and H5N1 viruses.展开更多
Introduction:The difficulty in treating lung adenocarcinoma(LUAD)is caused by a shortage of knowledge about the biological mechanisms and a lack of treatment choices.Objectives:The aim of this study was to identify a ...Introduction:The difficulty in treating lung adenocarcinoma(LUAD)is caused by a shortage of knowledge about the biological mechanisms and a lack of treatment choices.Objectives:The aim of this study was to identify a valuable molecular target for the treatment of LUAD.Methods:Using multiple databases,we screened for hub genes in LUAD using Cytoscape and explored the expression and prognosis of DLG associated protein 5(DLGAP5)in LUAD.We investigated the genetic variation,functional enrichment,and epigenetic activity of DLGAP5.Furthermore,we evaluated the relationship between the tumor microenvironment(TME)and DLGAP5.Results:Our study identified 10 hub genes in LUAD:CDC45,KIAA0101,DLGAP5,CDT1,NCAPG,CCNB1,CDCA5,CDC20,KIF11,and AURKA.We discovered that DLGAP5 was overexpressed and associated with poor prognosis in LUAD.DLGAP5 exhibited an overall genetic variation frequency of 2%,and its DNA promoter was hypomethylated in LUAD(p<0.05).The expression of DLGAP5 in LUAD showed a positive correlation with the majority of N6-methyladenosine(m6A)-methylation genes.Additionally,DLGAP5 was primarily associated with the cell cycle in LUAD.Notably,there was a significant favorable association between DLGAP5 and CD274,CTLA4,HAVCR2,and LAG3 in LUAD.Conclusion:DLGAP5 may be a therapeutic target for LUAD,as it affects cancer cells proliferation and development through the regulation of cell-cycle checkpoints and modulation of immune cell infiltration and immune checkpoints in the TME.展开更多
AIM: To investigate the contribution of variants of CARD15, OCTN1/2 and DLG5 genes in disease predispo- sition and phenotypes in a large Italian cohort of pediatric patients with inflammatory bowel diseases (IBD). MET...AIM: To investigate the contribution of variants of CARD15, OCTN1/2 and DLG5 genes in disease predispo- sition and phenotypes in a large Italian cohort of pediatric patients with inflammatory bowel diseases (IBD). METHODS: Two hundred patients with Crohn’s disease (CD), 186 ulcerative colitis (UC) patients, 434 par- ents (217 trios), and 347 healthy controls (HC) were studied. Polymorphisms of the three major variants of CARD15, 1672C/T and -207G/C SNPs for OCTN genes, IGR2096a_1 and IGR2198a_1 SNPs for the IBD5 locus, and 113G/A variant of the DLG5 gene were evaluated. Potential correlations with clinical sub-phenotypes were investigated. RESULTS: Polymorphisms of CARD15 were significantly associated with CD, and at least one variant was found in 38% of patients (15% in HC, OR = 2.7, P < 0.001). Homozygosis for both OCTN1/2 variants was more com- mon in CD patients (1672TT 24%, -207CC 29%) than in HC (16% and 21%, respectively; P = 0.03), with an in- creased frequency of the TC haplotype (44.8% vs 38.3% in HC, P = 0.04). No association with the DLG5 variant was found. CD carriers of OCTN1/2 and DLG5 variants more frequently had penetrating disease (P = 0.04 and P = 0.01), while carriers of CARD15 more frequently had ileal localization (P = 0.03). No gene-gene interaction was found. In UC patients, the TC haplotype was morefrequent (45.4%, P = 0.03), but no genotype/phenotype correlation was observed. CONCLUSION: Polymorphisms of CARD15 and OCTN genes, but not DLG5 are associated with pediatric on- set of CD. Polymorphisms of CARD15, OCTN, and DLG5 genes exert a weak influence on CD phenotype.展开更多
Castor is one of the top 10 oil crops in the world and has extremely valuable uses.Castor inflorescences directly affect yield,so the study of inflorescence development is very important in increasing castor yield.Our...Castor is one of the top 10 oil crops in the world and has extremely valuable uses.Castor inflorescences directly affect yield,so the study of inflorescence development is very important in increasing castor yield.Our previous studies have shown that the PIP5K gene family(PIP5Ks)is associated with inflorescence development.In this study,to determine the function of each PIP5K gene in castor,a female Lm-type castor line,aLmAB2,was used to determine the relative expression levels of the PIP5Ks in castor inflorescences.Six PIP5K genes were heterologously overexpressed in Arabidopsis thaliana,the relative expression of each gene and the effect on plants was determined in A.thaliana,and the relationships among the PIP5Ks in castor were inferred.The expression levels of the PIP5Ks in the female Lm-type castor line aLmAB2 were analyzed.The relative expression levels of the PIP5K9 and PIP5K11 genes were high(p<0.05)in isofemale inflorescences,and those of PIP5K1,PIP5K2,PIP5K6,and PIP5K8 were high(p<0.05)in female inflorescences but low(p<0.05)in bisexual inflorescences.The PIP5Ks were heterologously overexpressed in A.thaliana,and T3-generation plants with stable genetic resistance,i.e.,AT-PIP5K^(+)plants(AT-PIP5K1^(+),AT-PIP5K2^(+),AT-PIP5K6^(+),AT-PIP5K8^(+),AT-PIP5K9^(+),and ATPIP5K11^(+) plants),were obtained.Biological tests of the AT-PIP5K+plants showed that the growth of the main stem was significantly delayed in AT-PIP5K+plants compared with Columbia wild-type(WT)A.thaliana plants;the PIP5K1 and PIP5K2 genes promoted lateral stem growth and flower and silique development;and the PIP5K6,PIP5K8,PIP5K9 and PIP5K11 genes inhibited lateral stem growth and flower and silique development.The correlations among PIP5Ks in castor suggest that there may be a synergistic relationship among PIP5K1,PIP5K2,and PIP5K6 in castor inflorescences,and PIP5K8,PIP5K9,and PIP5K11 are complementary to the other three genes.展开更多
Mouse Dnajc5b and Cymg1 genes are new genes that we cloned specifically in mouse testis.Dnajc5b is a homolog of DNAJ(HSP40),subfamily C,and the second of member 5,so named Dnajc5b,which is located on chromosome 3 of m...Mouse Dnajc5b and Cymg1 genes are new genes that we cloned specifically in mouse testis.Dnajc5b is a homolog of DNAJ(HSP40),subfamily C,and the second of member 5,so named Dnajc5b,which is located on chromosome 3 of mouse and contains five exons with a total length of 947 bp.The reading frame is 597 bp and encodes a total of 199 amino acids.Dnajc5b was specifically expressed in mouse testis as shown by multi-tissue RT-PCR.Dnajc5b was weakly expressed in the first week and the second week after the mice were born,and the expression was enhanced in the third week.The greatest expression was in the eighth week of sexual maturity.At the same time,in situ hybridization results showed that Dnajc5b gene was specifically expressed in mouse spermatogonia,and its expression was positively correlated with testicular development.Cymg1(GenBank accession No.AY600990),which has a full length of 0.78 kb,and contains four exons and three introns,was cloned from a mouse testis cDNA library.The gene is located in the 2G3 area of chromosome 2.The full cDNA encompasses the entire open reading frame,encoding 141 amino acid residues.CYMG1 has a 44%(48/108)identity with mouse CRES and 30%(42/140)identity with mouse cystatin C.Northern blot analysis showed that the Cymg1 is specifically expressed in adult mouse testes.Immunohistochemistry revealed that the CYMG1 protein was expressed in mouse testes spermatogonium,spermatocytes,round spermatids,elongating spermatids and spermatozoa.RT-PCR results also showed that Cymg1 was expressed in mouse testes and spermatogonium.The Cymg1 expression level varied in different developmental stages.The Cymg1 expression level in the testes over different developmental stages correlates with the mouse spermatogenesis and sexual maturation process.展开更多
Mucin genes are the main component of mucus. The sea anemone species, Aulactinia veratra (Phylum Cnidaria) contains different types of mucin genes. In the intertidal zone, A. veratra is found to be exposed to air duri...Mucin genes are the main component of mucus. The sea anemone species, Aulactinia veratra (Phylum Cnidaria) contains different types of mucin genes. In the intertidal zone, A. veratra is found to be exposed to air during the low tide and produces large quantities of mucus as an external covering. The relation between low tide and mucus secretion is still unclear, and what is the role of mucin during arial exposure is not yet investigated. This study hypothesised that the mucin genes in A. veratra would have significantly high expression in response to aerial exposure. Therefore, the aim of current study was to examine and analyses the response of A. veratra mucins in response to an experiment involving three hours of aerial exposure. To achieve this, aim the RNA-sequencing and bioinformatics analyses were used to examine the expression profile of A. veratra mucin genes in response to aerial exposure. The generated results have shown that, Mucin4-like and mucin5B-like were up-regulated in response to the three hours of aerial exposure in A. veratra. This finding shows a significant role of mucin5B-like and mucin4-like genes in response to air stress at low tide. The data generated from this study could be used in conjunction with future mucin gene studies of sea anemones and other cnidarians to compare A. veratra mucin gene expression results across time, and to extend our understanding of mucin stress response in this phylum.展开更多
In order to reveal variation and revolution of NP genes of human avian H5 N1 influenza virus strains, the NP gene of a human avian H5 N1 influenza virus strain in Guangdong was sequenced and the global NP genes of str...In order to reveal variation and revolution of NP genes of human avian H5 N1 influenza virus strains, the NP gene of a human avian H5 N1 influenza virus strain in Guangdong was sequenced and the global NP genes of strains were retrieved. The sequences were analyzed by DNAStar 5.0, and the evolutionary speed was studied with reference to the epidemiological data. It was found that NP genes of 45 strains during 1997-2006 were homologically classified into three groups： strains in 1997-1998, strains in 2004-2005 and strains from 2003 to 2006. There were 35 substitutions in NPs in all strains accounting for a ratio of 7.03% （35/498）. An additional glycoprotein domain （NGT430-432） was found in NP genes in the strains of 2003-2006, the mutation of N370S in GD-01-06 resulted in occurrence of one more glycoprotein domain （NES368-370）. In the synonymous variation, Ks values in NP were 2.03 × 10^-5-2.55 × 10^-5 Nt/d and K. values in NP were 1.58 × 10^-6-3.10 × 10^-6 Nt/d. There didn＇t exist obviously selective pressure. An additional glycoprotein domain in every strain of 2003-2006 and one more in strain GD-01-06 might change the antigenicity of human avian H5 N1 influenza virus. The variation on human avian H5 N1 influenza strains occurred frequently in the natural world, which would result in high probability of human-human transmission along with the natural evolution of the virus.展开更多
Given that lactoferrin(LF)exerts an excellent protection of intestinal homeostasis,the underlying mechanisms,especially epigenetic regulations,are still unknown.This study aimed to investigate the effects of dietary L...Given that lactoferrin(LF)exerts an excellent protection of intestinal homeostasis,the underlying mechanisms,especially epigenetic regulations,are still unknown.This study aimed to investigate the effects of dietary LF epigenetically modulates the oxidative genes by histone modifications to ameliorate ileum inflammation of mice exposed to DON contaminated diet.As expected,we found in the morphology analysis that DON exposure increased ileum crypt depth(CD)and villus width(VW)but reduced villus height(VH)and VH:CD ratio compared to those of the vehicle group.Consistently,the elevated ROS and MDA,along with the decreased ATP,SOD,CAT,GSH,and complex I,III,V were observed in the DON-exposed mice ileum.In contrast,LF markedly ameliorated the impairments of morphological and biochemical indexes.Next,we conducted transcriptome analysis to explore the changed signaling pathways using the ileum RNA of the mice treated with DON or LF.Firstly,the cell cycle pathway genes were significantly downregulated in the DON-exposed mice,and LF improved the cell cycle profile.Again,gene ontology analysis showed that inflammation and oxidative stress were significantly activated by DON exposure,and these were recovered when the DON-exposed mice were supplemented with an LF diet.Consistent with these findings,the signaling pathways of the reduced oxidative phosphorylation and elevated TNFαwere also observed to be ameliorated by LF treatment.Importantly,histone modifications,including acetylation,methylation,and lactylation were suggested to be the vital players involved in the DON or LF treatment,in which LF significantly increased the loss of histone modifications on these genes.With a bioinformatics analysis and validation by qRT-PCR,the nuclear receptor NR5A2 was selected as a key master in the ileum of mice stimulated by DON.LF performed the benefit function on the NR5A2-mediated oxidative stress genes Ncoa4 and Prdx3 in the DON-exposed mice.Moreover,a ChIP-qPCR was used to verify that histone marks involving H3K9ac,H3K18ac,H3k27ac,H3K4me1,H3K9la,and H3K18la facilitated the epigenetic regulation of NR5A2-modulated actions.We conclude that dietary LF effectively ameliorated ileum lesions induced by DON in mice by modulating oxidative genes Ncoa4 and Prdx3 through histone modifications.展开更多
Background： Etomidate （R- 1 -[ 1 -ethylphenyl] imidazole-5-ethyl ester） is a widely used anesthetic drug that had been reported to contribute to cognitive deficits after general surgery. However, its underlying mec...Background： Etomidate （R- 1 -[ 1 -ethylphenyl] imidazole-5-ethyl ester） is a widely used anesthetic drug that had been reported to contribute to cognitive deficits after general surgery. However, its underlying mechanisms have not been fully elucidated. In this study, we aimed to explore the neurohiological mechanisms of cognitive impairments that caused by etomidate. Methods： A total of 30 Sprague-Dawley rats were used and divided into two groups randomly to receive a single injection ofeiomidate or vehicle. Then, the rats＇ spatial memory ability and neuronal survival were evaluated using the Morris water maze test and Nissl staining, respectively. Furthermore, we analyzed levels of oxidative stress, as well as cyclic adenosine 3＇,5＇-monophosphate response element-binding （CREB） protein phosphorylation and immediate early gene （IEG, including Arc, c-fos, and Egrl） expression levels using Western blot analysis. Results： Compared with vehicle-treated rats, the etomidate-treated rats displayed impaired spatial learning （day 4：27.26 ± 5.33 s vs. 35.52 ± 3.88s, t 2.988, P 0.0068; day 5： 15.84±4.02svs.30.67±4.23s,t=3.013,P=0.0057;day6：9.47±2.35svs.25.66±4.16s,t=3.567, P = 0.0036） and menaory ability （crossing times： 4.40 ± 1.18 vs. 2.06 ± 0.80, t = 2.896, P 0.0072; duration： 34.00± 4.24 s vs. 18.07 ±4.79 s, t = 3.023, P= 0.0053; total swimming distance： 40.73 ±3.45 cm vs. 27.40± 6.56 cm, t = 2.798, P = 0.0086） but no neuronal death. Furthermore, etomidate did not cause oxidative stress or deficits in CREB phosphorylation. The levels of multiple lEGs （Arc： vehicle treated rats 100%, etomidate treated rats 86%, t = 2.876, P 0.0086; c-los： Vehicle treated rats 100%, etomidate treated rats 72%, t =2.996, P = 0.0076; Egrl ： Vehicle treated rats 100%, etomidate treated rats 58%, t = 3.011, P=0.0057） were significantly reduced in hippocampi ofetomidate-treated rats. Conclusion： Our data suggested that etomidate might induce memory impairment in rats via inhibition of lEG expression.展开更多
基金supported by the National Key R&D Program of China(2022YFF1000100,2023YFD1300300)the National Natural Science Foundation of China(31572388,31972525)the China Agriculture Research System of MOF and MARA(CARS-41)。
文摘Background Chickens and ducks are vital sources of animal protein for humans.Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species,highlighting the need for more comprehensive genomes.The bird genome has more than tens of microchromosomes,but comparative genomics,annotations,and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies.We aim to complete the chicken and duck genomes,recover missing genes,and reveal common and unique chromosomal features between birds.Results The near telomere-to-telomere genomes of Silkie Gallus gallus and Mallard Anas platyrhynchos were successfully assembled via multiple high-coverage complementary technologies,with quality values of 36.65 and 44.17 for Silkie and Mallard,respectively;and BUSCO scores of 96.55%and 96.97%for Silkie and Mallard,respectively;the mapping rates reached over 99.52%for both assembled genomes,these evaluation results ensured high completeness and accuracy.We successfully annotated 20,253 and 19,621 protein-coding genes for Silkie and Mallard,respectively,and assembled gap-free sex chromosomes in Mallard for the first time.Comparative analysis revealed that microchromosomes differ from macrochromosomes in terms of GC content,repetitive sequence abundance,gene density,and levels of 5mC methylation.Different types of arrangements of centromeric repeat sequence centromeres exist in both Silkie and the Mallard genomes,with Mallard centromeres being invaded by CR1.The highly heterochromatic W chromosome,which serves as a refuge for ERVs,contains disproportionately long ERVs.Both Silkie and the Mallard genomes presented relatively high 5mC methylation levels on sex chromosomes and microchromosomes,and the telomeres and centromeres presented significantly higher 5mC methylation levels than the whole genome.Finally,we recovered 325 missing genes via our new genomes and annotated TNFA in Mallard for the first time,revealing conserved protein structures and tissue-specific expression.Conclusions The near telomere-to-telomere assemblies in Mallard and Silkie,with the first gap-free sex chromosomes in ducks,significantly enhanced our understanding of genetic structures in birds,specifically highlighting the distinctive chromosome features between the chicken and duck genomes.This foundational work also provides a series of newly identified missing genes for further investigation.
文摘目的:研究CHRNA5亚基突变对尼古丁受体功能的影响。方法:通过RT-PCR克隆CHRNA5基因片段,并通过重叠延伸PCR方法对CHRNA5亚基基因定点突变,从而构建CHRNA5突变型及野生型表达载体,然后转染至HEK293T细胞中,检测其基因表达。并将其分别与CHRNA3和CHRNB4共转至HEK293T细胞中,检测三质粒共转后的基因表达;通过采用尼古丁持续灌流细胞10 min,然后检测细胞内钙离子内流峰值的变化情况,接下来检测突变对转染后细胞活力的影响。结果:构建的CHRNA5表达载体在转染HEK293T细胞48 h后,能够检测到绿色荧光蛋白的表达,这证明重组载体已成功转染进HEK293T细胞;通过RT-PCR检测出转染细胞CHRNA5 m RNA表达,这证明CHRNA5突变型和野生型均在HEK293T细胞中成功进行了表达。通过尼古丁灌流细胞实验显示突变组和野生型组F340/F380峰值变化均值分别为0.865±0.048和0.447±0.127,突变体组峰值显著高于野生型组(P<0.05)。细胞活力检测实验发现0.01 m M和0.1 m M尼古丁刺激下突变组的细胞活力峰值分别为139%和137%,显著高于野生组的124%和126%,有显著差异(P<0.05)。结论:本研究成功构建了CHRNA5突变及野生型真核表达载体,发现CHRNA5的突变会导致其受体功能性改变,并影响细胞活力。
文摘Polymerase chain reaction(PCR) was used to amplify 5S rRNA spacer from wild rice(Oryza rufipogon and O.nivara) and cultivated rice(indica and japonica varieties of O.sativa L).The results show that there is spacer length variation within and between species,and the typical indica and japonica varieties have their unique banding patterns of amplified 5S rRNA spacers,whereas intermediate showed no specific amplification profile of spacer regions.The 5S rRNA genes in intermediate are either identical with that of indica variety or that of japonica variety.These data suggest that the spacer length polymorphisms can be used to distinguish between closely ralated species and subspecies.
基金supported by grants from the Department of Public Health of Hubei Province of China (No. 2012Z-B08)the Health Bureau of Wuhan City of China (No. WX12C10)
文摘Summary： This study investigated the effects of benazepril administered in the morning or evening on the diurnal variation of renin-angiotensin-aldosterone system （RAAS） and clock genes in the kidney. The male Wistar rat models of 5/6 subtotal nephrectomy （STNx） were established. Animals were ran- domly divided into 4 groups： sham STNx group （control）, STNx group, morning benazepril group （MB） and evening benazepril group （EB）. Benazepril was intragastfically administered at a dose of 10 mg/kg/day at 07：00 and 19：00 in the MB group and EB group respectively for 12 weeks. All the animals were synchronized to the light：dark cycle of 12：12 for 12 weeks. Systolic blood pressure （SBP）, 24-h urinary protein excretion and renal function were measured at 11 weeks. Blood samples and kidneys were collected every 4 h throughout a day to detect the expression pattern of renin activity （RA）, angio- tensin Ⅱ （Ang Ⅱ ） and aldosterone （Aid） by radioimmunoassay （RIA） and the mRNA expression profile of clock genes （bmall, dbp and per2） by real-time PCR at 12 weeks. Our results showed that no signifi- cant differences were noted in the SBP, 24-h urine protein excretion and renal function between the MB and EB groups. There were no significant differences in average Aid and RA content of a day between the MB group and EB group. The expression peak of bmall mRNA was phase-delayed by 4 to 8 h, and the diurnal variation of per2 and dbp mRNA diminished in the MB and EB groups compared with the control and STNx groups. It was concluded when the similar SBP reduction, RAAS inhibition and clock gene profile were achieved with optimal dose of benazepril, morning versus evening dosing of benazepril has the same renoprotection effects.
基金supported by the Western Light Project of Chinese Academy of Sciencesthe National Natural Science Foundation of China(31060057)the National Natural Science Foundation of Inner Mongolia,China(2015MS0305)
文摘Reference genes, stably expressing in different tissues and cells, are commonly used as the references in expression analysis. Selecting the optimum reference gene is crucial to the success of experiments. In this study, the expression stabilities of nine common reference genes, including ACT2, 18 S r RNA, APRT, EF-1α, RNA POL II, TUBα, TUBβ, GAPDH and TLF of Agropyron mongolicum, were studied under drought condition. Among them, 18 S r RNA was found to be the most optimum reference gene under drought stress by the analyzing of ge Norm and Norm Finder software. Quantitative expression levels of P5 CS using 18 S r RNA as the reference gene, and proline contents under drought stress in A. mongolicum were further operated, and we found the expression level of P5 CS gene and proline content had a significantly positive relationship（R^2=0.7763, P〈0.05）. This study established and validated 18 S r RNA as the reference genes in A. mongolicum under drought stress, providing a powerful tool for the quantitative expression analysis of drought genes in A. mongolicum.
基金funded by the National Natural Science Foundation of China(31471176)the Fundamental Research Funds for the Central Universities,China(15054034)
文摘H5N1 influenza represents one of the great challenges to public health.Some H5N1 viruses(i.e.,A/goose/Hubei/65/05,GS/65) are weakly pathogenic,while the others(i.e.,A/duck/Hubei/49/05,DK/49) are highly pathogenic to their natural hosts.Here,we performed brain and spleen transcriptomic analyses of control ducks and ones infected by the DK/49 or the GS/65 H5N1 virus.We demonstrated that,compared to the GS/65 virus,the DK/49 virus infection changed more numerous immune genes’ expression and caused continuous increasing of immune pathways(i.e.,RIG-I and MDA5) in ducks.We found that both H5N1 virus strains might escape or subvert host immune response through affecting alternative translation of immune genes,while the DK/49 virus seemed to induce alternative translation of more immune genes than the GS/65 virus.We also identified five co-expressional modules associated with H5N1 virus replication through the weight correlation network analysis(WGCNA).Moreover,we first demonstrated that the duck BCL2 L15 and DCSTAMP in one of these five modules inhibited both the highly pathogenic and weakly pathogenic H5N1 virus replication efficiently.These analyses,in combination with our comprehensive transcriptomic data,provided global view of the molecular architecture for the interaction between host and H5N1 viruses.
基金funded by the supporting funds for scientific research of the Sixth Affiliated Hospital,Sun Yat-sen University(P20200217202404781).
文摘Introduction:The difficulty in treating lung adenocarcinoma(LUAD)is caused by a shortage of knowledge about the biological mechanisms and a lack of treatment choices.Objectives:The aim of this study was to identify a valuable molecular target for the treatment of LUAD.Methods:Using multiple databases,we screened for hub genes in LUAD using Cytoscape and explored the expression and prognosis of DLG associated protein 5(DLGAP5)in LUAD.We investigated the genetic variation,functional enrichment,and epigenetic activity of DLGAP5.Furthermore,we evaluated the relationship between the tumor microenvironment(TME)and DLGAP5.Results:Our study identified 10 hub genes in LUAD:CDC45,KIAA0101,DLGAP5,CDT1,NCAPG,CCNB1,CDCA5,CDC20,KIF11,and AURKA.We discovered that DLGAP5 was overexpressed and associated with poor prognosis in LUAD.DLGAP5 exhibited an overall genetic variation frequency of 2%,and its DNA promoter was hypomethylated in LUAD(p<0.05).The expression of DLGAP5 in LUAD showed a positive correlation with the majority of N6-methyladenosine(m6A)-methylation genes.Additionally,DLGAP5 was primarily associated with the cell cycle in LUAD.Notably,there was a significant favorable association between DLGAP5 and CD274,CTLA4,HAVCR2,and LAG3 in LUAD.Conclusion:DLGAP5 may be a therapeutic target for LUAD,as it affects cancer cells proliferation and development through the regulation of cell-cycle checkpoints and modulation of immune cell infiltration and immune checkpoints in the TME.
文摘AIM: To investigate the contribution of variants of CARD15, OCTN1/2 and DLG5 genes in disease predispo- sition and phenotypes in a large Italian cohort of pediatric patients with inflammatory bowel diseases (IBD). METHODS: Two hundred patients with Crohn’s disease (CD), 186 ulcerative colitis (UC) patients, 434 par- ents (217 trios), and 347 healthy controls (HC) were studied. Polymorphisms of the three major variants of CARD15, 1672C/T and -207G/C SNPs for OCTN genes, IGR2096a_1 and IGR2198a_1 SNPs for the IBD5 locus, and 113G/A variant of the DLG5 gene were evaluated. Potential correlations with clinical sub-phenotypes were investigated. RESULTS: Polymorphisms of CARD15 were significantly associated with CD, and at least one variant was found in 38% of patients (15% in HC, OR = 2.7, P < 0.001). Homozygosis for both OCTN1/2 variants was more com- mon in CD patients (1672TT 24%, -207CC 29%) than in HC (16% and 21%, respectively; P = 0.03), with an in- creased frequency of the TC haplotype (44.8% vs 38.3% in HC, P = 0.04). No association with the DLG5 variant was found. CD carriers of OCTN1/2 and DLG5 variants more frequently had penetrating disease (P = 0.04 and P = 0.01), while carriers of CARD15 more frequently had ileal localization (P = 0.03). No gene-gene interaction was found. In UC patients, the TC haplotype was morefrequent (45.4%, P = 0.03), but no genotype/phenotype correlation was observed. CONCLUSION: Polymorphisms of CARD15 and OCTN genes, but not DLG5 are associated with pediatric on- set of CD. Polymorphisms of CARD15, OCTN, and DLG5 genes exert a weak influence on CD phenotype.
基金National Natural Science Foundation of China(31860071)Ministry of Education New Agricultural Research and Reform Practice Program(2020114)+4 种基金Surface Program of Inner Mongolia Natural Science Foundation(2021MS03008)Inner Mongolia Autonomous Region Grassland Talent Innovation Team-Rolling Support Program for Castor Molecular Breeding Research Innovation Talent Teams(2022)2023 Inner Mongolia Autonomous Region Science and Technology Department Establishes the Project of Key Laboratory Construction of Castor Breeding and Comprehensive Utilization in Inner Mongolia Autonomous RegionInner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region Project(237)Open Fund Project of Castor Industry Collaborative Innovation Center of Inner Mongolia Autonomous Region(MDK2021011,MDK2022014).
文摘Castor is one of the top 10 oil crops in the world and has extremely valuable uses.Castor inflorescences directly affect yield,so the study of inflorescence development is very important in increasing castor yield.Our previous studies have shown that the PIP5K gene family(PIP5Ks)is associated with inflorescence development.In this study,to determine the function of each PIP5K gene in castor,a female Lm-type castor line,aLmAB2,was used to determine the relative expression levels of the PIP5Ks in castor inflorescences.Six PIP5K genes were heterologously overexpressed in Arabidopsis thaliana,the relative expression of each gene and the effect on plants was determined in A.thaliana,and the relationships among the PIP5Ks in castor were inferred.The expression levels of the PIP5Ks in the female Lm-type castor line aLmAB2 were analyzed.The relative expression levels of the PIP5K9 and PIP5K11 genes were high(p<0.05)in isofemale inflorescences,and those of PIP5K1,PIP5K2,PIP5K6,and PIP5K8 were high(p<0.05)in female inflorescences but low(p<0.05)in bisexual inflorescences.The PIP5Ks were heterologously overexpressed in A.thaliana,and T3-generation plants with stable genetic resistance,i.e.,AT-PIP5K^(+)plants(AT-PIP5K1^(+),AT-PIP5K2^(+),AT-PIP5K6^(+),AT-PIP5K8^(+),AT-PIP5K9^(+),and ATPIP5K11^(+) plants),were obtained.Biological tests of the AT-PIP5K+plants showed that the growth of the main stem was significantly delayed in AT-PIP5K+plants compared with Columbia wild-type(WT)A.thaliana plants;the PIP5K1 and PIP5K2 genes promoted lateral stem growth and flower and silique development;and the PIP5K6,PIP5K8,PIP5K9 and PIP5K11 genes inhibited lateral stem growth and flower and silique development.The correlations among PIP5Ks in castor suggest that there may be a synergistic relationship among PIP5K1,PIP5K2,and PIP5K6 in castor inflorescences,and PIP5K8,PIP5K9,and PIP5K11 are complementary to the other three genes.
基金Hunan Provincial Natural Science Foundation of China(No.2017JJ2109).
文摘Mouse Dnajc5b and Cymg1 genes are new genes that we cloned specifically in mouse testis.Dnajc5b is a homolog of DNAJ(HSP40),subfamily C,and the second of member 5,so named Dnajc5b,which is located on chromosome 3 of mouse and contains five exons with a total length of 947 bp.The reading frame is 597 bp and encodes a total of 199 amino acids.Dnajc5b was specifically expressed in mouse testis as shown by multi-tissue RT-PCR.Dnajc5b was weakly expressed in the first week and the second week after the mice were born,and the expression was enhanced in the third week.The greatest expression was in the eighth week of sexual maturity.At the same time,in situ hybridization results showed that Dnajc5b gene was specifically expressed in mouse spermatogonia,and its expression was positively correlated with testicular development.Cymg1(GenBank accession No.AY600990),which has a full length of 0.78 kb,and contains four exons and three introns,was cloned from a mouse testis cDNA library.The gene is located in the 2G3 area of chromosome 2.The full cDNA encompasses the entire open reading frame,encoding 141 amino acid residues.CYMG1 has a 44%(48/108)identity with mouse CRES and 30%(42/140)identity with mouse cystatin C.Northern blot analysis showed that the Cymg1 is specifically expressed in adult mouse testes.Immunohistochemistry revealed that the CYMG1 protein was expressed in mouse testes spermatogonium,spermatocytes,round spermatids,elongating spermatids and spermatozoa.RT-PCR results also showed that Cymg1 was expressed in mouse testes and spermatogonium.The Cymg1 expression level varied in different developmental stages.The Cymg1 expression level in the testes over different developmental stages correlates with the mouse spermatogenesis and sexual maturation process.
文摘Mucin genes are the main component of mucus. The sea anemone species, Aulactinia veratra (Phylum Cnidaria) contains different types of mucin genes. In the intertidal zone, A. veratra is found to be exposed to air during the low tide and produces large quantities of mucus as an external covering. The relation between low tide and mucus secretion is still unclear, and what is the role of mucin during arial exposure is not yet investigated. This study hypothesised that the mucin genes in A. veratra would have significantly high expression in response to aerial exposure. Therefore, the aim of current study was to examine and analyses the response of A. veratra mucins in response to an experiment involving three hours of aerial exposure. To achieve this, aim the RNA-sequencing and bioinformatics analyses were used to examine the expression profile of A. veratra mucin genes in response to aerial exposure. The generated results have shown that, Mucin4-like and mucin5B-like were up-regulated in response to the three hours of aerial exposure in A. veratra. This finding shows a significant role of mucin5B-like and mucin4-like genes in response to air stress at low tide. The data generated from this study could be used in conjunction with future mucin gene studies of sea anemones and other cnidarians to compare A. veratra mucin gene expression results across time, and to extend our understanding of mucin stress response in this phylum.
文摘In order to reveal variation and revolution of NP genes of human avian H5 N1 influenza virus strains, the NP gene of a human avian H5 N1 influenza virus strain in Guangdong was sequenced and the global NP genes of strains were retrieved. The sequences were analyzed by DNAStar 5.0, and the evolutionary speed was studied with reference to the epidemiological data. It was found that NP genes of 45 strains during 1997-2006 were homologically classified into three groups： strains in 1997-1998, strains in 2004-2005 and strains from 2003 to 2006. There were 35 substitutions in NPs in all strains accounting for a ratio of 7.03% （35/498）. An additional glycoprotein domain （NGT430-432） was found in NP genes in the strains of 2003-2006, the mutation of N370S in GD-01-06 resulted in occurrence of one more glycoprotein domain （NES368-370）. In the synonymous variation, Ks values in NP were 2.03 × 10^-5-2.55 × 10^-5 Nt/d and K. values in NP were 1.58 × 10^-6-3.10 × 10^-6 Nt/d. There didn＇t exist obviously selective pressure. An additional glycoprotein domain in every strain of 2003-2006 and one more in strain GD-01-06 might change the antigenicity of human avian H5 N1 influenza virus. The variation on human avian H5 N1 influenza strains occurred frequently in the natural world, which would result in high probability of human-human transmission along with the natural evolution of the virus.
基金funded by Jiangsu Higher Education Key Natural Science Research Program(21 KJA230002)Yangzhou Hanjiang sci-tech project.Jiangsu Higher Education Key Natural Science Research Program,21 KJA230002,Dejun Ji,Yangzhou Hanjiang sci-tech project。
文摘Given that lactoferrin(LF)exerts an excellent protection of intestinal homeostasis,the underlying mechanisms,especially epigenetic regulations,are still unknown.This study aimed to investigate the effects of dietary LF epigenetically modulates the oxidative genes by histone modifications to ameliorate ileum inflammation of mice exposed to DON contaminated diet.As expected,we found in the morphology analysis that DON exposure increased ileum crypt depth(CD)and villus width(VW)but reduced villus height(VH)and VH:CD ratio compared to those of the vehicle group.Consistently,the elevated ROS and MDA,along with the decreased ATP,SOD,CAT,GSH,and complex I,III,V were observed in the DON-exposed mice ileum.In contrast,LF markedly ameliorated the impairments of morphological and biochemical indexes.Next,we conducted transcriptome analysis to explore the changed signaling pathways using the ileum RNA of the mice treated with DON or LF.Firstly,the cell cycle pathway genes were significantly downregulated in the DON-exposed mice,and LF improved the cell cycle profile.Again,gene ontology analysis showed that inflammation and oxidative stress were significantly activated by DON exposure,and these were recovered when the DON-exposed mice were supplemented with an LF diet.Consistent with these findings,the signaling pathways of the reduced oxidative phosphorylation and elevated TNFαwere also observed to be ameliorated by LF treatment.Importantly,histone modifications,including acetylation,methylation,and lactylation were suggested to be the vital players involved in the DON or LF treatment,in which LF significantly increased the loss of histone modifications on these genes.With a bioinformatics analysis and validation by qRT-PCR,the nuclear receptor NR5A2 was selected as a key master in the ileum of mice stimulated by DON.LF performed the benefit function on the NR5A2-mediated oxidative stress genes Ncoa4 and Prdx3 in the DON-exposed mice.Moreover,a ChIP-qPCR was used to verify that histone marks involving H3K9ac,H3K18ac,H3k27ac,H3K4me1,H3K9la,and H3K18la facilitated the epigenetic regulation of NR5A2-modulated actions.We conclude that dietary LF effectively ameliorated ileum lesions induced by DON in mice by modulating oxidative genes Ncoa4 and Prdx3 through histone modifications.
文摘Background： Etomidate （R- 1 -[ 1 -ethylphenyl] imidazole-5-ethyl ester） is a widely used anesthetic drug that had been reported to contribute to cognitive deficits after general surgery. However, its underlying mechanisms have not been fully elucidated. In this study, we aimed to explore the neurohiological mechanisms of cognitive impairments that caused by etomidate. Methods： A total of 30 Sprague-Dawley rats were used and divided into two groups randomly to receive a single injection ofeiomidate or vehicle. Then, the rats＇ spatial memory ability and neuronal survival were evaluated using the Morris water maze test and Nissl staining, respectively. Furthermore, we analyzed levels of oxidative stress, as well as cyclic adenosine 3＇,5＇-monophosphate response element-binding （CREB） protein phosphorylation and immediate early gene （IEG, including Arc, c-fos, and Egrl） expression levels using Western blot analysis. Results： Compared with vehicle-treated rats, the etomidate-treated rats displayed impaired spatial learning （day 4：27.26 ± 5.33 s vs. 35.52 ± 3.88s, t 2.988, P 0.0068; day 5： 15.84±4.02svs.30.67±4.23s,t=3.013,P=0.0057;day6：9.47±2.35svs.25.66±4.16s,t=3.567, P = 0.0036） and menaory ability （crossing times： 4.40 ± 1.18 vs. 2.06 ± 0.80, t = 2.896, P 0.0072; duration： 34.00± 4.24 s vs. 18.07 ±4.79 s, t = 3.023, P= 0.0053; total swimming distance： 40.73 ±3.45 cm vs. 27.40± 6.56 cm, t = 2.798, P = 0.0086） but no neuronal death. Furthermore, etomidate did not cause oxidative stress or deficits in CREB phosphorylation. The levels of multiple lEGs （Arc： vehicle treated rats 100%, etomidate treated rats 86%, t = 2.876, P 0.0086; c-los： Vehicle treated rats 100%, etomidate treated rats 72%, t =2.996, P = 0.0076; Egrl ： Vehicle treated rats 100%, etomidate treated rats 58%, t = 3.011, P=0.0057） were significantly reduced in hippocampi ofetomidate-treated rats. Conclusion： Our data suggested that etomidate might induce memory impairment in rats via inhibition of lEG expression.
