Objective:To investigate the effect of Guangdong Shenqu(GSQ)on intestinal flora structure in mice with food stagnation through 16S rDNA sequencing.Methods: Mice were randomly assigned to control,model,GSQ low-dose(GSQ...Objective:To investigate the effect of Guangdong Shenqu(GSQ)on intestinal flora structure in mice with food stagnation through 16S rDNA sequencing.Methods: Mice were randomly assigned to control,model,GSQ low-dose(GSQL),GSQ medium-dose(GSQM),GSQ high-dose(GSQH),and lacidophilin tablets(LAB)groups,with each group containing 10 mice.A food stagnation and internal heat mouse model was established through intragastric administration of a mixture of beeswax and olive oil(1:15).The control group was administered normal saline,and the model group was administered beeswax and olive oil to maintain a state.The GSQL(2 g/kg),GSQM(4 g/kg),GSQH(8 g/kg),and LAB groups(0.625 g/kg)were administered corresponding drugs for 5 d.After administration,16S rDNA sequencing was performed to assess gut microbiota in mouse fecal samples.Results: The model group exhibited significant intestinal flora changes.Following GSQ administration,the abundance and diversity index of the intestinal flora increased significantly,the number of bacterial species was regulated,andαandβdiversity were improved.GSQ administration increased the abundance of probiotics,including Clostridia,Lachnospirales,and Lactobacillus,whereas the abundance of conditional pathogenic bacteria,such as Allobaculum,Erysipelotrichaceae,and Bacteroides decreased.Functional prediction analysis indicated that the pathogenesis of food stagnation and GSQ intervention were primarily associated with carbohydrate,lipid,and amino acid metabolism,among other metabolic pathways.Conclusion: The digestive mechanism of GSQ may be attributed to its role in restoring diversity and abundance within the intestinal flora,thereby improving the composition and structure of the intestinal flora in mice and subsequently influencing the regulation of metabolic pathways.展开更多
Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matc...Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matched paraneoplastic normal tissues, and to explore the intrinsic mechanism of OSCC development and progres- sion. We obtained the differentially expressed mRNA expression profiles in 10 pairs of fresh-frozen OSCC tissue specimens and matched paraneoplastic normal tissue specimens by high-throughput RNA sequencing. By using Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses, the functional significance of the differentially expressed genes were analyzed. We identified 1,120 sig- nificantly up-regulated mRNAs and 178 significantly down-regulated mRNAs in OSCC, compared to normal tissue. The differentially expressed mRNAs were involved in 20 biological processes and 68 signal pathways. Compared to adjacent normal tissue, the expression of MAGEAll was up-regulated; TCHH was down-regulated. These find- ings were verified by real-time PCR. These differentially expressed mRNAs may function as oncogenes or tumor suppressors in the development and progression of OSCC. This study provides novel insights into OSCC. However, further work is needed to determine if these differentially expressed mRNAs have potential roles as diagnostic bio- markers and candidate therapeutic targets for OSCC.展开更多
This study aims to investigate the effect of a magnetic field on nitrous oxide(N2O)emission from a sequencing batch reactor treating low-strength domestic wastewater at low temperature(10℃).After running for 124 days...This study aims to investigate the effect of a magnetic field on nitrous oxide(N2O)emission from a sequencing batch reactor treating low-strength domestic wastewater at low temperature(10℃).After running for 124 days in parallel,results indicated that the conversion rate of N2O for a magnetic field-sequencing batch reactor(MF-SBR)decreased by34.3%compared to that of a conventional SBR(C-SBR).Meanwhile,the removal efficiencies for total nitrogen(TN)and ammonia nitrogen(NH4-N)of the MF-SBR were 22.4%and 39.5%higher than those of the C-SBR.High-throughput sequencing revealed that the abundances of AOB(Nitrosomonas),NOB(Nitrospira)and denitrifiers(Zoogloea),which could reduce N2O to N2,were promoted significantly in the MF-SBR.Enzyme activities(Nir)and gene abundances(nos Z nir S and nir K)for denitrification in the MF-SBR were also notably higher compared to C-SBR.Our study shows that application of a magnetic field is a useful approach for inhibiting the generation of N2O and promoting the nitrogen removal efficiency by affecting the microbial characteristics of sludge in an SBR treating domestic wastewater at low temperature.展开更多
In a previous study,we found that long non-coding genes in Alzheimer’s disease(AD)are a result of endogenous gene disorders caused by the recruitment of microRNA(miRNA)and mRNA,and that miR-200a-3p and other represen...In a previous study,we found that long non-coding genes in Alzheimer’s disease(AD)are a result of endogenous gene disorders caused by the recruitment of microRNA(miRNA)and mRNA,and that miR-200a-3p and other representative miRNAs can mediate cognitive impairment and thus serve as new biomarkers for AD.In this study,we investigated the abnormal expression of miRNA and mRNA and the pathogenesis of AD at the epigenetic level.To this aim,we performed RNA sequencing and an integrative analysis of the cerebral cortex of the widely used amyloid precursor protein and presenilin-1 double transgenic mouse model of AD.Overall,129 mRNAs and 68 miRNAs were aberrantly expressed.Among these,eight down-regulated miRNAs and seven up-regulated miRNAs appeared as promising noninvasive biomarkers and therapeutic targets.The main enriched signaling pathways involved mitogen-activated kinase protein,phosphatidylinositol 3-kinase-protein kinase B,mechanistic target of rapamycin kinase,forkhead box O,and autophagy.An miRNA-mRNA network between dysregulated miRNAs and corresponding target genes connected with AD progression was also constructed.These miRNAs and mRNAs are potential biomarkers and therapeutic targets for new treatment strategies,early diagnosis,and prevention of AD.The present results provide a novel perspective on the role of miRNAs and mRNAs in AD.This study was approved by the Experimental Animal Care and Use Committee of Institute of Medicinal Biotechnology of Beijing,China(approval No.IMB-201909-D6)on September 6,2019.展开更多
supported in part by grants from the Strategic Priority Research Program of Chinese Academy of Sciences （XDB15010103）;the National Natural Science Foundation of China （41201247）
Ovarian endometrioma(OE),also known as“chocolate cysts,”is a cystic mass that develops in the ovaries due to endometriosis and is a common gynecological condition characterized by the growth of endometrial tissue ou...Ovarian endometrioma(OE),also known as“chocolate cysts,”is a cystic mass that develops in the ovaries due to endometriosis and is a common gynecological condition characterized by the growth of endometrial tissue outside the uterus,leading to symptoms such as dysmenorrhea,pelvic pain,and infertility.However,the precise molecular and cellular mechanisms driving this pathophysiology remain largely unknown,posing challenges for diagnosis and treatment.Here,we employed integrated single-cell transcriptomic profiling of over 52,000 individual cells from endometrial tissues of OE patients and healthy donors and identified twelve major cell populations.We identified notable alterations in cell type-specific proportions and molecular signatures associated with OE.Notably,the activation of IGFBP5^(+) macrophages with pro-inflammatory properties,NK cell exhaustion,and aberrant proliferation of IQCG^(+) and KLF2^(+) epithelium are key features and may be the potential mechanisms underlying the pathogenesis of OE.Collectively,our data contribute to a better understanding of OE at the single cell level and may pave the way for the development of novel therapeutic strategies.展开更多
BACKGROUND Autism spectrum disorders(ASD)represent a substantial social problem affecting at least 1 in 100 children worldwide.These conditions are very often accompanied by intellectual disability(ID)and speech delay...BACKGROUND Autism spectrum disorders(ASD)represent a substantial social problem affecting at least 1 in 100 children worldwide.These conditions are very often accompanied by intellectual disability(ID)and speech delay;thus,they can be considered within a clinical continuum of neurodevelopmental disorders.Given the high heterogeneity of ASD,the subjective nature of diagnostic criteria,and the presence of phenocopies,identifying genetic determinants of these disorders remains a challenge.AIM To investigate the spectrum and frequency of rare genetic variants in genes with proven association with ASD in Russian children.METHODS 110 patients from 106 families were recruited into the study mean age at diagnosis 6 years;boy-to-girl ratio 3:1.Most of the patients(84%)demonstrated a combination of ASD with developmental delay(DD)or ID.Patients with syndromic features were subjected to the chromosomal microarray analysis.The remained children underwent clinical exome sequencing aimed at identifying presumably monogenic causes of ASD.The study focused on rare(minor allele frequency≤0.001)variants affecting high-confidence ASD-associated genes.RESULTS Pathogenic copy number variations were detected in three(7%)of the patients examined.Clinical exome sequencing revealed pathogenic/likely pathogenic variants in 12 of 105 cases(11%),indicating the presence of monogenic syndromes with established clinical significance(Pitt-Hopkins syndrome,ZTTK syndrome,syndromic X-linked ID of Billuart type,Snijders-Blok-Campeau,Helsmoortel-van der Aa,Coffin-Siris,Clark-Baraitser,Keefstra syndromes,etc.).In addition,27 patients(26%)had 37 rare variants of unknown clinical significance in DSCAM,SHANK2,AUTS2,ADNP,ANKRD11,APBA2,ARID1B,ASTN2,ATRX,SCN1A,CHD2,DEAF1,EHMT1,GRIN2B,NBEA,NR4A2,TRIO,TRIP12,POGZ,EP300,FOXP1,PCDH19,GRIN2A,NCKAP1,and CHD8 genes.No specific variant was detected more than once in unrelated patients.Among the genes with rare variants found in 2 or more patients were TRIP12(n=4),AUTS2(n=3),ARID1B(n=3),PCDH19(n=3),EP300(n=3),TRIO(n=2),ASTN2(n=2),EHMT1(n=2),and CHD2(n=2).Of note,5 male ASD/DD patients from 3 unrelated families had PCDH19 missense variants,confirming that at least some hemizygous males with non-mosaic PCDH19 variants may present with neurobehavioral abnormalities.These variants did not cause epilepsy restricted to females in patients’mothers or sisters.CONCLUSION These data confirm a tremendous diversity of genetic causes of ASD.Clinical exome sequencing may serve as a reasonable alternative to whole-exome sequencing.展开更多
AIM To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea.METHODS Following 2 d of adaptive feeding, 12 specific pathogenfree Kunming mice were ra...AIM To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea.METHODS Following 2 d of adaptive feeding, 12 specific pathogenfree Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics(23.33 m L·kg^(-1)·d^(-1)) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units(OTUs) was carried outafter amplification and sequencing.RESULTS OTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups(P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32 C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively.CONCLUSION Antibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.展开更多
The genome sequence information in combination with DNA microarrays promises to revolutionize the way of cellu-lar and molecular biological research by allowing complex mixtures of RNA and DNA to interrogated in a par...The genome sequence information in combination with DNA microarrays promises to revolutionize the way of cellu-lar and molecular biological research by allowing complex mixtures of RNA and DNA to interrogated in a parallel and quantita-tive fashion. DNA microarrays can be used to measure levels of gene expression for tens of thousands of gene simultane-ously and take advantage of all available sequence information for experimental design and data interpretation in pursuit of biological understanding. Recent progress in experimental genomics allows DNA microarrays not simply to provide a cata-logue of all the genes and information about their function, but to understand how the components work together to comprise functioning cells and organisms. This brief review gives a survey of DNA microarrays technology and its applications in ge-nome and gene function analysis, gene expression studies, biological signal and defense system, cell cycle regulation, mechanism of transcriptional regulation, proteomics, and the functionality of food component.展开更多
This study investigated differences in the community structure and environmental responses of the bacterial community in sediments of the Bohai Sea.Illumina high-throughput sequencing technology and real-time PCR were...This study investigated differences in the community structure and environmental responses of the bacterial community in sediments of the Bohai Sea.Illumina high-throughput sequencing technology and real-time PCR were used to assay the bacterial 16S rRNA genes in the surface sediments of 13 sampling stations in the Bohai Sea.The results showed that sediments at the majority of the 13 sampling stations were contaminated by heavy metal mercury.The main phyla of bacteria recorded included Proteobacteria(52.92%),Bacteroidetes(11.76%),Planctomycetes(7.39%),Acidobacteria(6.53%)and Chloroflexi(4.97%).The genus with the highest relative abundance was Desulfobulbus(4.99%),which was the dominant genus at most sampling stations,followed by Lutimonas and Halioglobus.The main factors influencing bacterial community structure were total organic carbon,followed by depth and total phosphorus.The content of lead,cadmium,chromium,copper and zinc had a consistent effect on community structure.Arsenic showed a negative correlation with bacterial community structure in most samples,while the impact of mercury on community structure was not significant.The bacterial community in sediment samples from the Bohai Sea was rich in diversity and displayed an increase in diversity from high to low latitudes.The data indicated that the Bohai Sea had abundant microbial resources and was rich in bacteria with the potential to metabolize many types of pollutants.展开更多
The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood. In this study, the jaundice model was established by bile duct ligation （BDL） in mice, and differenti...The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood. In this study, the jaundice model was established by bile duct ligation （BDL） in mice, and differential gene expression patterns were analyzed in the lower thoracic spinal cord involved in cholestatic pruritus after BDL operation using high-throughput RNA sequencing. At 21st day after BDL, the expression levels of ENSRNOG00000060523, ENSRNOG00000058405 and ENSRNOG00000055193 mRNA were significantly up-regulated, and those of ENSRNOG00000042197, ENSRNOG00000008478, ENSRNOG00000019607, ENSRNOG00000020647, ENSRNOG00000046289, Gemin8, Serpina3n and Trim63 mRNA were significantly down-regulated in BDL group. The RNAseq data of selected mRNAs were validated by RT-qPCR. The expression levels of ENSRNOG00000042197, ENSRNOG00000008478, ENSRNOG00000019607, ENSRNOG00000020647, ENSRNOG00000046289 and Serpina3n mRNA were significantly down-regulated in BDL group. This study suggested that cholestatic pruritus in experimental obstructive jaundice mouse model is related with in the changes of gene expression profiles in spinal cord.展开更多
Objective To investigate the genetic causes of sudden sensorineural hearing loss(SSNHL)patients in China.This study focused on analyzing variations of coding sequence of common genes related to deafness,revealing the ...Objective To investigate the genetic causes of sudden sensorineural hearing loss(SSNHL)patients in China.This study focused on analyzing variations of coding sequence of common genes related to deafness,revealing the molecular pathogenesis of sudden deafness from a genomics perspective,discovering molecular markers associated with the onset of deafness,and then supplying prevention to high-risk populations,classifying disease according to accurate etiology,and choosing a much more precision therapy.Methods We retrospectively analyzed the clinical characteristics of 51 patients diagnosed as SSNHL with vertigo treated in the Chinese PLA General Hospital.In this study,mutation screening of 307 nuclear genes and mitochondrial genome responsible for human or mouse deafness was performed on the 51 cases of unilateral sudden deafness patients with vertigo.Results We identified 51 cases of unilateral sudden deafness,including 2 cases of low-mid frequency hearing impairment,18 cases of mid-high frequency hearing loss,11 cases of flat-type hearing loss,and 20 cases of all frequency hearing loss.Among the 51 cases,8(15.69%)cases of GJB2 heterozygous variations,1(1.96%)case of GJB3 heterozygous variations,5(9.8%)cases of SLC26A4 heterozygous variations,2(3.92%)cases of COCH heterozygous variations,14(27.45%)cases of CDH23 heterozygous variations,14(27.45%)cases of OTOF heterozygous variations,1(1.96%)case of SLC17A8 heterozygous variations and 2(3.92%)cases of KCNE1 heterozygous variations.No mtDNA gene variations were identified.Conclusion SSNHL has some relationship with hereditary in Chinese population,but its complex genetic pathogenic mechanisms need further study.展开更多
Micro RNAs(mi RNAs) have been shown to play critical regulatory roles in gene expression in cotton. Although a large number of mi RNAs have been identified in cotton fibers, the functions of mi RNAs in seed developmen...Micro RNAs(mi RNAs) have been shown to play critical regulatory roles in gene expression in cotton. Although a large number of mi RNAs have been identified in cotton fibers, the functions of mi RNAs in seed development remain unexplored. In this study, a small RNA library was constructed from cotton seeds sampled at 15 days post-anthesis(DPA) and was subjected to high-throughput sequencing. A total of 95 known mi RNAs were detected to be expressed in cotton seeds. The expression pattern of these identified mi RNAs was profiled and 48 known mi RNAs were differentially expressed between cotton seeds and fibers at 15 DPA. In addition, 23 novel mi RNA candidates were identified in 15-DPA seeds. Putative targets for 21 novel and 87 known mi RNAs were successfully predicted and 900 expressed sequence tag(EST) sequences were proposed to be candidate target genes, which are involved in various metabolic and biological processes, suggesting a complex regulatory network in developing cotton seeds. Furthermore, mi RNA-mediated cleavage of three important transcripts in vivo was validated by RLM-5′ RACE. This study is the first to show the regulatory network of mi RNAs that are involved in developing cotton seeds and provides a foundation for future studies on the specific functions of these mi RNAs in seed development.展开更多
Background:Chemotherapy is the mainstay to treat metastatic colorectal cancer(CRC).However,a sizeable proportion of patients do not respond to treatment,which leads to the recurrence of disease.This study was carried ...Background:Chemotherapy is the mainstay to treat metastatic colorectal cancer(CRC).However,a sizeable proportion of patients do not respond to treatment,which leads to the recurrence of disease.This study was carried out to identify reliable gene expression-based marker(s)to predict the response to chemotherapy and the risk of recurrence.Methods:This prospective study involved the collection of tumor tissues(n=100)and normal tissues(n=10)from CRC patients who primarily underwent surgical treatment.Global gene expression profiles were generated on microarray(Affymetrix;n=5)and the next-generation sequencing(NGS)(Illumina;n=20)platforms.Patients were classified as responders(n=13;complete response with no relapse)or non-responders(n=12;recurrence of disease leading to death).Common dysregulated genes identified from both platforms were replicated in an independent set(n=75;quantitative real-time polymerase chain reaction(q RT-PCR)).The area under the curve(AUC)was generated,and a combinatorial analysis was performed.Results:A total of 193 and 1351 genes were dysregulated in microarray and NGS datasets,respectively.Of the top common genes(PTGIS,LYVE1,C3,C7,CXCL12,CEACAM6,MUC13,and ST14)that were selected for replication,upregulation of five genes(PTGIS,C3,C7,LYVE1,and CXCL12)were associated with the non-responder group in validation set.Combinatorial analysis and comparison of AUC identified a significant increase(p=0.03)in AUC by 15.2%(95%confidence interval(CI):0.01-0.29)for two genes(PTGIS and LYVE1).Sensitivity,specificity,positive predictive value(PPV),and negative predictive value(NPV)were88.9%,100%,100%,and 95.6%,respectively.Conclusion:Assessing upregulation of the PTGIS and LYVE1 genes enables identification of individuals who may not respond to adjuvant chemotherapy and the risk of recurrence.The addition of drugs targeting these genes may improve response and benefit the patients.展开更多
基金supported by the National Natural Science Foundation of China(81872995).
文摘Objective:To investigate the effect of Guangdong Shenqu(GSQ)on intestinal flora structure in mice with food stagnation through 16S rDNA sequencing.Methods: Mice were randomly assigned to control,model,GSQ low-dose(GSQL),GSQ medium-dose(GSQM),GSQ high-dose(GSQH),and lacidophilin tablets(LAB)groups,with each group containing 10 mice.A food stagnation and internal heat mouse model was established through intragastric administration of a mixture of beeswax and olive oil(1:15).The control group was administered normal saline,and the model group was administered beeswax and olive oil to maintain a state.The GSQL(2 g/kg),GSQM(4 g/kg),GSQH(8 g/kg),and LAB groups(0.625 g/kg)were administered corresponding drugs for 5 d.After administration,16S rDNA sequencing was performed to assess gut microbiota in mouse fecal samples.Results: The model group exhibited significant intestinal flora changes.Following GSQ administration,the abundance and diversity index of the intestinal flora increased significantly,the number of bacterial species was regulated,andαandβdiversity were improved.GSQ administration increased the abundance of probiotics,including Clostridia,Lachnospirales,and Lactobacillus,whereas the abundance of conditional pathogenic bacteria,such as Allobaculum,Erysipelotrichaceae,and Bacteroides decreased.Functional prediction analysis indicated that the pathogenesis of food stagnation and GSQ intervention were primarily associated with carbohydrate,lipid,and amino acid metabolism,among other metabolic pathways.Conclusion: The digestive mechanism of GSQ may be attributed to its role in restoring diversity and abundance within the intestinal flora,thereby improving the composition and structure of the intestinal flora in mice and subsequently influencing the regulation of metabolic pathways.
基金supported by a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD,2014-37)
文摘Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matched paraneoplastic normal tissues, and to explore the intrinsic mechanism of OSCC development and progres- sion. We obtained the differentially expressed mRNA expression profiles in 10 pairs of fresh-frozen OSCC tissue specimens and matched paraneoplastic normal tissue specimens by high-throughput RNA sequencing. By using Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses, the functional significance of the differentially expressed genes were analyzed. We identified 1,120 sig- nificantly up-regulated mRNAs and 178 significantly down-regulated mRNAs in OSCC, compared to normal tissue. The differentially expressed mRNAs were involved in 20 biological processes and 68 signal pathways. Compared to adjacent normal tissue, the expression of MAGEAll was up-regulated; TCHH was down-regulated. These find- ings were verified by real-time PCR. These differentially expressed mRNAs may function as oncogenes or tumor suppressors in the development and progression of OSCC. This study provides novel insights into OSCC. However, further work is needed to determine if these differentially expressed mRNAs have potential roles as diagnostic bio- markers and candidate therapeutic targets for OSCC.
基金supported by the Major Science and Technology Program for Water Pollution Control and Treatment(No.2017ZX07202-001-002)
文摘This study aims to investigate the effect of a magnetic field on nitrous oxide(N2O)emission from a sequencing batch reactor treating low-strength domestic wastewater at low temperature(10℃).After running for 124 days in parallel,results indicated that the conversion rate of N2O for a magnetic field-sequencing batch reactor(MF-SBR)decreased by34.3%compared to that of a conventional SBR(C-SBR).Meanwhile,the removal efficiencies for total nitrogen(TN)and ammonia nitrogen(NH4-N)of the MF-SBR were 22.4%and 39.5%higher than those of the C-SBR.High-throughput sequencing revealed that the abundances of AOB(Nitrosomonas),NOB(Nitrospira)and denitrifiers(Zoogloea),which could reduce N2O to N2,were promoted significantly in the MF-SBR.Enzyme activities(Nir)and gene abundances(nos Z nir S and nir K)for denitrification in the MF-SBR were also notably higher compared to C-SBR.Our study shows that application of a magnetic field is a useful approach for inhibiting the generation of N2O and promoting the nitrogen removal efficiency by affecting the microbial characteristics of sludge in an SBR treating domestic wastewater at low temperature.
基金This study was supported by the National Natural Science Foundation of China(General Program),No.81673411the United Fund Project of National Natural Science Foundation of China,No.U1803281+1 种基金Young Medical Talents Award Project of Chinese Academy of Medical Sciences,No.2018RC350013Chinese Academy of Medical Sciences Innovation Project for Medical Science,No.2017-I2M-1-016(all to RL).
文摘In a previous study,we found that long non-coding genes in Alzheimer’s disease(AD)are a result of endogenous gene disorders caused by the recruitment of microRNA(miRNA)and mRNA,and that miR-200a-3p and other representative miRNAs can mediate cognitive impairment and thus serve as new biomarkers for AD.In this study,we investigated the abnormal expression of miRNA and mRNA and the pathogenesis of AD at the epigenetic level.To this aim,we performed RNA sequencing and an integrative analysis of the cerebral cortex of the widely used amyloid precursor protein and presenilin-1 double transgenic mouse model of AD.Overall,129 mRNAs and 68 miRNAs were aberrantly expressed.Among these,eight down-regulated miRNAs and seven up-regulated miRNAs appeared as promising noninvasive biomarkers and therapeutic targets.The main enriched signaling pathways involved mitogen-activated kinase protein,phosphatidylinositol 3-kinase-protein kinase B,mechanistic target of rapamycin kinase,forkhead box O,and autophagy.An miRNA-mRNA network between dysregulated miRNAs and corresponding target genes connected with AD progression was also constructed.These miRNAs and mRNAs are potential biomarkers and therapeutic targets for new treatment strategies,early diagnosis,and prevention of AD.The present results provide a novel perspective on the role of miRNAs and mRNAs in AD.This study was approved by the Experimental Animal Care and Use Committee of Institute of Medicinal Biotechnology of Beijing,China(approval No.IMB-201909-D6)on September 6,2019.
基金supported in part by grants from the Strategic Priority Research Program of Chinese Academy of Sciences (XDB15010103)the National Natural Science Foundation of China (41201247)
文摘supported in part by grants from the Strategic Priority Research Program of Chinese Academy of Sciences （XDB15010103）;the National Natural Science Foundation of China （41201247）
基金supported from Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences(CI2023D003,CI2021B014)the National Key Research and Development Program of China(2022YFC2303600,2020YFA0908000)+8 种基金the Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine(ZYYCXTD-C-202002)the CACMS Innovation Fund(CI2023E002,CI2021A05101,CI2021A05104)the Science and Technology Foundation o f Shenzhen(JCYJ20210324115800001)the Science and Technology Foundation of Shenzhen(Shenzhen Clinical Medical Research Center for Geriatric Diseases)the Shenzhen Medical Research Fund(B2302051)the National Natural Science Foundation of China(82201786)Guangdong Basic and Applied Basic Research Foundation(2021A1515110646)Guangdong-Dongguan Joint Fund Regional Cultivation Project(2021B1515140033)Dongguan Science and Technology of Social Development Program(20211800904742,20221800905732,20221800904462).
文摘Ovarian endometrioma(OE),also known as“chocolate cysts,”is a cystic mass that develops in the ovaries due to endometriosis and is a common gynecological condition characterized by the growth of endometrial tissue outside the uterus,leading to symptoms such as dysmenorrhea,pelvic pain,and infertility.However,the precise molecular and cellular mechanisms driving this pathophysiology remain largely unknown,posing challenges for diagnosis and treatment.Here,we employed integrated single-cell transcriptomic profiling of over 52,000 individual cells from endometrial tissues of OE patients and healthy donors and identified twelve major cell populations.We identified notable alterations in cell type-specific proportions and molecular signatures associated with OE.Notably,the activation of IGFBP5^(+) macrophages with pro-inflammatory properties,NK cell exhaustion,and aberrant proliferation of IQCG^(+) and KLF2^(+) epithelium are key features and may be the potential mechanisms underlying the pathogenesis of OE.Collectively,our data contribute to a better understanding of OE at the single cell level and may pave the way for the development of novel therapeutic strategies.
基金Supported by the Russian Science Foundation Grant,No.24-45-00067.
文摘BACKGROUND Autism spectrum disorders(ASD)represent a substantial social problem affecting at least 1 in 100 children worldwide.These conditions are very often accompanied by intellectual disability(ID)and speech delay;thus,they can be considered within a clinical continuum of neurodevelopmental disorders.Given the high heterogeneity of ASD,the subjective nature of diagnostic criteria,and the presence of phenocopies,identifying genetic determinants of these disorders remains a challenge.AIM To investigate the spectrum and frequency of rare genetic variants in genes with proven association with ASD in Russian children.METHODS 110 patients from 106 families were recruited into the study mean age at diagnosis 6 years;boy-to-girl ratio 3:1.Most of the patients(84%)demonstrated a combination of ASD with developmental delay(DD)or ID.Patients with syndromic features were subjected to the chromosomal microarray analysis.The remained children underwent clinical exome sequencing aimed at identifying presumably monogenic causes of ASD.The study focused on rare(minor allele frequency≤0.001)variants affecting high-confidence ASD-associated genes.RESULTS Pathogenic copy number variations were detected in three(7%)of the patients examined.Clinical exome sequencing revealed pathogenic/likely pathogenic variants in 12 of 105 cases(11%),indicating the presence of monogenic syndromes with established clinical significance(Pitt-Hopkins syndrome,ZTTK syndrome,syndromic X-linked ID of Billuart type,Snijders-Blok-Campeau,Helsmoortel-van der Aa,Coffin-Siris,Clark-Baraitser,Keefstra syndromes,etc.).In addition,27 patients(26%)had 37 rare variants of unknown clinical significance in DSCAM,SHANK2,AUTS2,ADNP,ANKRD11,APBA2,ARID1B,ASTN2,ATRX,SCN1A,CHD2,DEAF1,EHMT1,GRIN2B,NBEA,NR4A2,TRIO,TRIP12,POGZ,EP300,FOXP1,PCDH19,GRIN2A,NCKAP1,and CHD8 genes.No specific variant was detected more than once in unrelated patients.Among the genes with rare variants found in 2 or more patients were TRIP12(n=4),AUTS2(n=3),ARID1B(n=3),PCDH19(n=3),EP300(n=3),TRIO(n=2),ASTN2(n=2),EHMT1(n=2),and CHD2(n=2).Of note,5 male ASD/DD patients from 3 unrelated families had PCDH19 missense variants,confirming that at least some hemizygous males with non-mosaic PCDH19 variants may present with neurobehavioral abnormalities.These variants did not cause epilepsy restricted to females in patients’mothers or sisters.CONCLUSION These data confirm a tremendous diversity of genetic causes of ASD.Clinical exome sequencing may serve as a reasonable alternative to whole-exome sequencing.
基金Supported by the National Natural Science Foundation of China,No.81573951
文摘AIM To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea.METHODS Following 2 d of adaptive feeding, 12 specific pathogenfree Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics(23.33 m L·kg^(-1)·d^(-1)) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units(OTUs) was carried outafter amplification and sequencing.RESULTS OTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups(P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32 C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively.CONCLUSION Antibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.
文摘The genome sequence information in combination with DNA microarrays promises to revolutionize the way of cellu-lar and molecular biological research by allowing complex mixtures of RNA and DNA to interrogated in a parallel and quantita-tive fashion. DNA microarrays can be used to measure levels of gene expression for tens of thousands of gene simultane-ously and take advantage of all available sequence information for experimental design and data interpretation in pursuit of biological understanding. Recent progress in experimental genomics allows DNA microarrays not simply to provide a cata-logue of all the genes and information about their function, but to understand how the components work together to comprise functioning cells and organisms. This brief review gives a survey of DNA microarrays technology and its applications in ge-nome and gene function analysis, gene expression studies, biological signal and defense system, cell cycle regulation, mechanism of transcriptional regulation, proteomics, and the functionality of food component.
基金The National Key Basic Research Special Foundation of China under contract No.2017YFC1404500the National Natural Science Foundation of China under contract No.41676115
文摘This study investigated differences in the community structure and environmental responses of the bacterial community in sediments of the Bohai Sea.Illumina high-throughput sequencing technology and real-time PCR were used to assay the bacterial 16S rRNA genes in the surface sediments of 13 sampling stations in the Bohai Sea.The results showed that sediments at the majority of the 13 sampling stations were contaminated by heavy metal mercury.The main phyla of bacteria recorded included Proteobacteria(52.92%),Bacteroidetes(11.76%),Planctomycetes(7.39%),Acidobacteria(6.53%)and Chloroflexi(4.97%).The genus with the highest relative abundance was Desulfobulbus(4.99%),which was the dominant genus at most sampling stations,followed by Lutimonas and Halioglobus.The main factors influencing bacterial community structure were total organic carbon,followed by depth and total phosphorus.The content of lead,cadmium,chromium,copper and zinc had a consistent effect on community structure.Arsenic showed a negative correlation with bacterial community structure in most samples,while the impact of mercury on community structure was not significant.The bacterial community in sediment samples from the Bohai Sea was rich in diversity and displayed an increase in diversity from high to low latitudes.The data indicated that the Bohai Sea had abundant microbial resources and was rich in bacteria with the potential to metabolize many types of pollutants.
文摘The spinal origin of cholestatic itch in experimental obstructive jaundice mouse model remains poorly understood. In this study, the jaundice model was established by bile duct ligation （BDL） in mice, and differential gene expression patterns were analyzed in the lower thoracic spinal cord involved in cholestatic pruritus after BDL operation using high-throughput RNA sequencing. At 21st day after BDL, the expression levels of ENSRNOG00000060523, ENSRNOG00000058405 and ENSRNOG00000055193 mRNA were significantly up-regulated, and those of ENSRNOG00000042197, ENSRNOG00000008478, ENSRNOG00000019607, ENSRNOG00000020647, ENSRNOG00000046289, Gemin8, Serpina3n and Trim63 mRNA were significantly down-regulated in BDL group. The RNAseq data of selected mRNAs were validated by RT-qPCR. The expression levels of ENSRNOG00000042197, ENSRNOG00000008478, ENSRNOG00000019607, ENSRNOG00000020647, ENSRNOG00000046289 and Serpina3n mRNA were significantly down-regulated in BDL group. This study suggested that cholestatic pruritus in experimental obstructive jaundice mouse model is related with in the changes of gene expression profiles in spinal cord.
基金supported by the National Natural Science Foundation of China(No.81830028,No.81900950 and No.81900951).
文摘Objective To investigate the genetic causes of sudden sensorineural hearing loss(SSNHL)patients in China.This study focused on analyzing variations of coding sequence of common genes related to deafness,revealing the molecular pathogenesis of sudden deafness from a genomics perspective,discovering molecular markers associated with the onset of deafness,and then supplying prevention to high-risk populations,classifying disease according to accurate etiology,and choosing a much more precision therapy.Methods We retrospectively analyzed the clinical characteristics of 51 patients diagnosed as SSNHL with vertigo treated in the Chinese PLA General Hospital.In this study,mutation screening of 307 nuclear genes and mitochondrial genome responsible for human or mouse deafness was performed on the 51 cases of unilateral sudden deafness patients with vertigo.Results We identified 51 cases of unilateral sudden deafness,including 2 cases of low-mid frequency hearing impairment,18 cases of mid-high frequency hearing loss,11 cases of flat-type hearing loss,and 20 cases of all frequency hearing loss.Among the 51 cases,8(15.69%)cases of GJB2 heterozygous variations,1(1.96%)case of GJB3 heterozygous variations,5(9.8%)cases of SLC26A4 heterozygous variations,2(3.92%)cases of COCH heterozygous variations,14(27.45%)cases of CDH23 heterozygous variations,14(27.45%)cases of OTOF heterozygous variations,1(1.96%)case of SLC17A8 heterozygous variations and 2(3.92%)cases of KCNE1 heterozygous variations.No mtDNA gene variations were identified.Conclusion SSNHL has some relationship with hereditary in Chinese population,but its complex genetic pathogenic mechanisms need further study.
基金supported by the National Basic Research Program of China(2010CB126003)the National Transgenic Animals and Plants Research Project(2011ZX08005-003,2011ZX08009-003)
文摘Micro RNAs(mi RNAs) have been shown to play critical regulatory roles in gene expression in cotton. Although a large number of mi RNAs have been identified in cotton fibers, the functions of mi RNAs in seed development remain unexplored. In this study, a small RNA library was constructed from cotton seeds sampled at 15 days post-anthesis(DPA) and was subjected to high-throughput sequencing. A total of 95 known mi RNAs were detected to be expressed in cotton seeds. The expression pattern of these identified mi RNAs was profiled and 48 known mi RNAs were differentially expressed between cotton seeds and fibers at 15 DPA. In addition, 23 novel mi RNA candidates were identified in 15-DPA seeds. Putative targets for 21 novel and 87 known mi RNAs were successfully predicted and 900 expressed sequence tag(EST) sequences were proposed to be candidate target genes, which are involved in various metabolic and biological processes, suggesting a complex regulatory network in developing cotton seeds. Furthermore, mi RNA-mediated cleavage of three important transcripts in vivo was validated by RLM-5′ RACE. This study is the first to show the regulatory network of mi RNAs that are involved in developing cotton seeds and provides a foundation for future studies on the specific functions of these mi RNAs in seed development.
基金supported by the Indian Council of Medical Research(ICMR),wide file no 54/04/2019-HUM/BMS(IRIS No.-IRIS Cell No–2019-0441)to Dr.Ravikanth Vishnubhotla(Principal Investigator)and Dr.Pradeep Rebala.Dr.Sanjeev M.Patil(Co-Investigators)
文摘Background:Chemotherapy is the mainstay to treat metastatic colorectal cancer(CRC).However,a sizeable proportion of patients do not respond to treatment,which leads to the recurrence of disease.This study was carried out to identify reliable gene expression-based marker(s)to predict the response to chemotherapy and the risk of recurrence.Methods:This prospective study involved the collection of tumor tissues(n=100)and normal tissues(n=10)from CRC patients who primarily underwent surgical treatment.Global gene expression profiles were generated on microarray(Affymetrix;n=5)and the next-generation sequencing(NGS)(Illumina;n=20)platforms.Patients were classified as responders(n=13;complete response with no relapse)or non-responders(n=12;recurrence of disease leading to death).Common dysregulated genes identified from both platforms were replicated in an independent set(n=75;quantitative real-time polymerase chain reaction(q RT-PCR)).The area under the curve(AUC)was generated,and a combinatorial analysis was performed.Results:A total of 193 and 1351 genes were dysregulated in microarray and NGS datasets,respectively.Of the top common genes(PTGIS,LYVE1,C3,C7,CXCL12,CEACAM6,MUC13,and ST14)that were selected for replication,upregulation of five genes(PTGIS,C3,C7,LYVE1,and CXCL12)were associated with the non-responder group in validation set.Combinatorial analysis and comparison of AUC identified a significant increase(p=0.03)in AUC by 15.2%(95%confidence interval(CI):0.01-0.29)for two genes(PTGIS and LYVE1).Sensitivity,specificity,positive predictive value(PPV),and negative predictive value(NPV)were88.9%,100%,100%,and 95.6%,respectively.Conclusion:Assessing upregulation of the PTGIS and LYVE1 genes enables identification of individuals who may not respond to adjuvant chemotherapy and the risk of recurrence.The addition of drugs targeting these genes may improve response and benefit the patients.
