Objective:To identify potential key genes associated with pre-eclampsia through bioinformatics analysis,construct predictive models using machine-learning algorithms,and evaluate the models'performance in predicti...Objective:To identify potential key genes associated with pre-eclampsia through bioinformatics analysis,construct predictive models using machine-learning algorithms,and evaluate the models'performance in predicting pre-eclampsia.Methods:Gene-expression microarray datasets GSE10588,GSE66273,and GSE30186 related to pre-eclampsia were downloaded from the gene expression omnibus(GEO).Data were normalized using R,and differentially expressed genes(DEGs)were identified.LASSO regression was applied to further filter DEGs.Based on the selected DEGs,six machine-learning models-logistic regression(LR),random forest(RF),support vector machine(SVM),K-nearest neighbors(KNN),neural network(NN),and eXtreme gradient boosting(XGBoost)were built in R,and their performance was validated.Results:From the three datasets,a total of 1,363 genes were extracted.LASSO regression narrowed these to 265 candidate key genes.Multivariate analysis ultimately identified four genes closely associated with pre-eclampsia:EVI5,GCLM,LEP,and SYNPO2L.Using these four key genes,six machine-learning models were constructed.Receiver operating characteristic(ROC)analysis showed that all models achieved AUC>0.9:LR(AUC=0.983,95%CI=0.942-0.998),RF(AUC=0.961,95%CI=0.912-0.987),SVM(AUC=0.936,95%CI=0.879-0.972),KNN(AUC=0.970,95%CI=0.924-0.992),NN(AUC=0.916,95%CI=0.854-0.958),and XGBoost(AUC=0.952,95%CI=0.900-0.982).There was no statistically significant difference among the AUCs of the models(P>0.05).Conclusion:This study identified four key genes linked to preeclampsia through integrated bioinformatics analysis.Predictive models built on these genes can accurately forecast the occurrence of pre-eclampsia,suggesting that the four genes may serve as potential biomarkers for early diagnosis and therapeutic targeting of pre-eclampsia.展开更多
Amphibian metamorphosis provides a wonderful model to study the thyroid hormone（TH）signaling disrupting activity of environmental chemicals, with Xenopus laevis as the most commonly used species. This study aimed to...Amphibian metamorphosis provides a wonderful model to study the thyroid hormone（TH）signaling disrupting activity of environmental chemicals, with Xenopus laevis as the most commonly used species. This study aimed to establish a rapid and sensitive screening assay based on TH-response gene expression analysis using Pelophylax nigromaculatus, a native frog species distributed widely in East Asia, especially in China. To achieve this, five candidate TH-response genes that were sensitive to T3 induction were chosen as molecular markers, and T3 induction was determined as 0.2 nmol/L T3 exposure for 48 hr. The developed assay can detect the agonistic activity of T3 with a lowest observed effective concentration of 0.001 nmol/L and EC50 at around 0.118–1.229 nmol/L, exhibiting comparable or higher sensitivity than previously reported assays. We further validated the efficiency of the developed assay by detecting the TH signaling disrupting activity of tetrabromobisphenol A（TBBPA）, a known TH signaling disruptor. In accordance with previous reports, we found a weak TH agonistic activity for TBBPA in the absence of T3,whereas a TH antagonistic activity was found for TBBPA at higher concentrations in the presence of T3, showing that the P. nigromaculatus assay is effective for detecting TH signaling disrupting activity. Importantly, we observed non-monotonic dose-dependent disrupting activity of TBBPA in the presence of T3, which is difficult to detect with in vitro reporter gene assays. Overall, the developed P. nigromaculatus assay can be used to screen TH signaling disrupting activity of environmental chemicals with high sensitivity.展开更多
Screening gene function in vivo is a powerful approach to discover novel drug targets. We present high-throughput screening （HTS） data for 3 762 distinct global gene knockout （KO） mouse lines with viable adult hom...Screening gene function in vivo is a powerful approach to discover novel drug targets. We present high-throughput screening （HTS） data for 3 762 distinct global gene knockout （KO） mouse lines with viable adult homozygous mice generated using either gene-trap or homologous recombination technologies. Bone mass was determined from DEXA scans of male and female mice at 14 weeks of age and by microCT analyses of bones from male mice at 16 weeks of age. Wild-type （WT） cagemates/littermates were examined for each gene KO. Lethality was observed in an additional 850 KO lines. Since primary HTS are susceptible to false positive findings, additional cohorts of mice from KO lines with intriguing HTS bone data were examined. Aging, ovariectomy, histomorphometry and bone strength studies were performed and possible non-skeletal phenotypes were explored. Together, these screens identified multiple genes affecting bone mass： 23 previously reported genes （Calcr, Cebpb, Crtap, Dcstamp, Dkkl, Duoxa2, Enppl, Fgf23, Kissl/Kisslr, Kl （Klotho）, Lrp5, Mstn, Neol, Npr2, Ostml, Postn, Sfrp4, S1c30a5, Sic39a13, Sost, Sumf1, Src, Wnt10b）, five novel genes extensively characterized （Cldn18, Fam20c, Lrrkl, Sgpll, Wnt16）, five novel genes with preliminary characterization （Agpat2, RassfS, Slc10a7, Stc26a7, Slc30a10） and three novel undisclosed genes coding for potential osteoporosis drug targets.展开更多
Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking a...Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking and gait. This disease can not be clearly identified through laboratory tests at present, thus application of high-throughput technique in studying the expression profiles of PD helps to find the genetic markers for its early diagnosis. Studies on expression profiles of neurodegenerative diseases have revealed the novel genes and pathways involved in the progress of illness. In this study, the expression profiles of PD in blood were compared, showing that 181 differentially expressed genes （DEG） exhibit a similar expression trend both in patients and in normal controls.展开更多
F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 o...F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 out of 75 F-box proteins have experimentally documented substrates, whereas in Drosophila 12 F-box proteins have been characterized with known substrates. To systematically investigate the genetic and molecular functions of F-box proteins in Drosophila, we performed a survey of the literature and databases. We identified 45 Drosophila genes that encode proteins containing at least one F-box domain. We collected publically available RNAi lines against these genes and used them in a tissue-specific RNAi-based phenotypic screen. Here, we present our systematic phenotypic dataset from the eye, the wing and the notum. This dataset is the first of its kind and represents a useful resource for future studies of the molecular and genetic functions of F-box genes in Drosophila. Our results show that, as expected, F-box genes in Drosophila have regulatory roles in a diverse array of processes including cell proliferation, cell growth, signal transduction, and cellular and animal survival.展开更多
Yersinia pestis is the causative agent of bubonic and pneumonic plagues. Strains of Y. pestis are classified into four biovars： antiqua, mediaevalis, orientalis, and microtus[11. There are two microtus-related plague...Yersinia pestis is the causative agent of bubonic and pneumonic plagues. Strains of Y. pestis are classified into four biovars： antiqua, mediaevalis, orientalis, and microtus[11. There are two microtus-related plague loci in China： the Microtus brandti plague focus in the Xilin Gol Grassland （focus L） and the Microtus fuscus plague focus in the Ojnghai-Tibet Plateau （focus M）.展开更多
Prenatal diagnosis was requested for an undiagnosed eye disease showing X-linked inheritance in a family. No medical records existed for the affected family members..Mapping of the X chromosome and candidate gene muta...Prenatal diagnosis was requested for an undiagnosed eye disease showing X-linked inheritance in a family. No medical records existed for the affected family members..Mapping of the X chromosome and candidate gene mutation screening identified a c.C267A[p.F89L] mutation in NPD previously described as possibly causing Norrie disease..The detection of the c.C267A[p.F89L] variant in another unrelated family confirms the pathogenic nature of the mutation for the Norrie disease phenotype. Gene mapping, haplotype analysis, and candidate gene screening have been previously utilized in research applications but were applied here in a diagnostic setting due to the scarcity of available clinical information..The clinical diagnosis and mutation identification were critical for providing proper genetic counseling and prenatal diagnosis for this family.展开更多
Purpose: To compare the sensitivity of Hexosaminidase A (HexA) enzyme-based testing to gene sequencing for carrier detection in non-Jewish individuals. Methods: Blood samples were obtained from parents and relatives o...Purpose: To compare the sensitivity of Hexosaminidase A (HexA) enzyme-based testing to gene sequencing for carrier detection in non-Jewish individuals. Methods: Blood samples were obtained from parents and relatives of affected patients at an annual Tay-Sachs and Allied Diseases Foundation meeting. A family history was taken for each individual. Samples were analyzed for leukocyte HexA activity, serum HexA activity and subjected to extensive gene sequencing. The results from these analyses were combined with our previously published data describing 34 obligate Tay-Sachs disease (TSD) carriers. Results: Twelve additional TSD carriers were detected in this study. Gene sequencing successfully identified all 12 carriers whereas enzyme analysis identified 11 of 12 carriers. This individual is a carrier of the B1 variant that is known to cause false negative results with enzyme testing. Combined data from 46 non-Jewish TSD carriers revealed that gene sequencing had a higher sensitivity rate than HexA enzyme-based testing (94% versus 87%) in non-Jewish TSD carriers. In our series, approximately 4% of non-Jewish TSD carriers have this mutation. Conclusions: HexA gene sequencing provides a higher sensitivity for TSD carrier detection than HexA based enzyme analysis in non-Jewish patients primarily due to the presence of individuals with the B1 variant.展开更多
Aim: To assess the clinical significance of hTERC amplification for cervical cancer screening detected by fluorescence in situ hybridization (FISH) and compare it with that of current screening methods within the same...Aim: To assess the clinical significance of hTERC amplification for cervical cancer screening detected by fluorescence in situ hybridization (FISH) and compare it with that of current screening methods within the same group. Methods: A total of one hundred and nine women were recruited in this study. All of them had liquid-based thin-prep cytologic test (TCT), human papillomavirus (HPV) DNA testing and hTERC gene amplification analysis using interphase two-color FISH. In addition, colposcopically directed biopsy and/or cone biopsy were conducted for definite histopathologic diagnosis for each case. The optimal threashold of hTERC gene amplification by fluorescence in situ hybridization (FISH) were assecced by receiver operating characteristic (ROC) curve. The results of hTERC gene amplification analysis were compared with the cytological analysis, HPV DNA testing and those of subsequent biopsies. Results: Among the 109 patients, 18 were benign lesion, 17 were LSIL, 66 were HSIL and 8 were invasive carcinoma of cervix (ICC). Of them, hTERC-positive cases were found in 0.0% (0/18) of normal specimens, 11.8% (2/17) of LSIL, 72.7% (48/66) of HSIL and 100.0% (8/8) of ICC, respectively. The positive rate of hTERC gene amplification was significantly higher in HSIL and ICC compared with normal and LSIL (all P < 0.01).The optimal cut-off point of percentages of cells with hTERC amplification was determined as 5.5%. Using this threshold the hTERC test reached a much higher specificity(94.3%, 33/35) and a relatively lower sensitivity(77.0%, 57/74) to distinguish benign lesion and LSIL from HSIL and ICC in comparison with HR-HPV test (51.4%;91.9%) and TCT (74.3%;81.1%). Area Under the Curve revealed that hTERC amplification test performed more accurately (area under the curve = 0.857) compared to HPV test (area under the curve = 0.717) and cytology(area under the curve = 0.777) to discriminate HSIL or higher from LSIL or lower. This study also found a significant positive correlation between positive hTERC gain and HR-HPV infection, abnormal cytological or histopathologic lesions (all P < 0.01) in patients with cervical diseases. Conclusion: hTERC amplification testing may be a promising adjunct to screen women for cervical precancer or cancer with high specificity and accuracy.展开更多
Wolman disease is a rare autosomal recessive disorder caused by mutations in the LIPA gene (10q23.31). The LIPA gene encodes lysosomal acid lipase (LAL), which plays a key role in hydrolysis of the cholesteryl esters ...Wolman disease is a rare autosomal recessive disorder caused by mutations in the LIPA gene (10q23.31). The LIPA gene encodes lysosomal acid lipase (LAL), which plays a key role in hydrolysis of the cholesteryl esters and triglycerides. Two unrelated families from Bulgaria were referred for genetic testing with clinical diagnosis Wolman disease. Sanger sequencing of all coding exons and exon-intron boundaries of the LIPA gene was performed. The index patients were found to be homozygous for two different mutations in the LIPA gene: a missense mutation, c.260G > T, p.Gly87Val, which affects the enzyme active site and a splice-site change, c.822+1G > A, which most probably destroys the enzyme polypeptide chain. These two completely different types of mutations along the LIPA gene resulted in a very similar phenotype involving liver, kidney, gastrointestinal, muscle and blood disturbances. As consanguinity is not typical for the Bulgarian population, a possible explanation of the homozygosity could be presence of endemic regions for given mutations. To check this hypothesis, selective screening for these mutations was performed in two presumable endemic regions in Bulgaria. Altogether, 100 newborns were screened for p.Gly87Val mutation and the detected carrier frequency was about 1% (1/100), while in the group of 100 newborns screened for the c.822 + 1G > A mutation the detected carrier frequency was 2% (2/100). The results indicate a high recurrence risk of Wolman disease in these particular Bulgarian regions of about 1:10000. These findings are from crucial importance for the inhabitants of the corresponding parts of Bulgaria. They may benefit from early genetic testing and adequate genetic counselling during family planning.展开更多
以高耐热性玉米品种郑单958、低耐热性玉米品种先玉335为试验材料,以正常生长条件为对照(CK),利用半自动伸缩高温棚进行花期高温胁迫(HT)处理,通过circRNA高通量测序筛选高温胁迫下不同玉米品种花粉中差异表达的环状RNA(circRNA),对其...以高耐热性玉米品种郑单958、低耐热性玉米品种先玉335为试验材料,以正常生长条件为对照(CK),利用半自动伸缩高温棚进行花期高温胁迫(HT)处理,通过circRNA高通量测序筛选高温胁迫下不同玉米品种花粉中差异表达的环状RNA(circRNA),对其来源基因进行GO和KEGG富集分析,并筛选具有miRNA结合位点的差异表达circRNA,预测其下游目的基因,分析玉米花粉中响应高温胁迫的潜在circRNA-miRNA-mRNA共表达调控网络,从多层面解析玉米花粉中调控高温胁迫的分子作用机制,为提高玉米品种的耐热性提供理论依据。结果表明,在郑单958、先玉335不同样本中共鉴定出1 843个不同的circRNA,它们在玉米染色体中的分布不同。每个circRNA所包含的外显子数目也不相同,其中,大多数(624个)circRNA只含有1个外显子。在郑单958花粉中共鉴定出1 563个circRNA,其中,CK958-1、CK958-2、CK958-3中分别鉴定出305、213、356个circRNA,HT958-1、HT958-2、HT958-3中分别鉴定出222、242、225个circRNA。在先玉335花粉中共鉴定出1 423个circRNA,其中,CK335-1、CK335-2、CK335-3中分别鉴定出272、188、229个circRNA,HT335-1、HT335-2、HT335-3中分别鉴定出259、237、238个circRNA。不同样本中占比最高的均为外显子circRNA。circRNA与其来源基因不是一一对应的关系,有748个circRNA来源基因通过反向剪接机制只形成1个circRNA,156个circRNA来源基因通过反向剪接机制各自形成2个circRNA。在郑单958高温胁迫花粉与对照花粉对比组(HT958 vs CK958)中共筛选到9个差异表达circRNA,其中2个circRNA呈上调表达,其来源基因显著富集到焦磷酸酶活性、核苷酸磷酸代谢过程、糖基磷脂酰肌醇(GPI)锚定代谢过程等17个GO条目,显著富集到GPI锚定生物合成、代谢途径等KEGG通路。在先玉335高温胁迫花粉与对照花粉对比组(HT335 vs CK335)中共筛选到1个差异表达circRNA,其来源基因没有显著富集到任何GO条目、KEGG通路。在郑单958高温胁迫花粉与先玉335高温胁迫花粉对比组(HT958 vs HT335)中共筛选到17个差异表达circRNA,其中6个circRNA呈上调表达,其来源基因显著富集到内质网系统、高尔基相关囊泡膜、膜蛋白水解等16个GO条目中,没有显著富集到任何KEGG代谢通路。5个circRNA具有miRNA结合位点,可以作为海绵岛吸附miRNA间接调控下游靶标基因的表达,构建了包括5个circRNA、5个不同家族miRNA、2个mRNA在内的circRNA-miRNA-mRNA共表达调控网络。筛选到了54个circRNA包含内部核糖体进入位点(IRES),可以翻译表达多肽或者蛋白质直接作用于靶标基因。展开更多
Moebius syndrome is a rare disorder primarily characterized by congenital facial palsy, frequently accompanied by ocular abduction anomalies and occasionally associated with orofacial, limb and musculoskeletal malform...Moebius syndrome is a rare disorder primarily characterized by congenital facial palsy, frequently accompanied by ocular abduction anomalies and occasionally associated with orofacial, limb and musculoskeletal malformations. Abnormal development of cranial nerves Ⅴ through Ⅻ underlines the disease pathogenesis. Although a genetic etiology for Moebius syndrome was proposed, molecular genetic studies to identify the causative gene（s） are scarce. In this study, we selected two candidate genes. One is BASP1 residing in a human chromosome 5p15.1-p15.2, syntenic to mouse chromosome 15qA2-qB2, to which a mouse model with facial nerve anomalies was mapped. The other is transcribed processed pseudogene TPψg-BASP1, which is located on chromosome 13q flanking the putative locus for Moebius syndrome and might be involved in the regulation of the transcripts encoded by BASP1. Mutation analyses in nineteen patients excluded these genes as being candidates for Moebius syndrome.展开更多
Objective:To determine whether a new-born child from a family carrying a deafness gene needs cochlear implantation to avoid dysphonia by screening and sequencing a deafness-related gene.Results:Both screening and sequ...Objective:To determine whether a new-born child from a family carrying a deafness gene needs cochlear implantation to avoid dysphonia by screening and sequencing a deafness-related gene.Results:Both screening and sequencing results confirmed that the new born child had a normal GJB2 gene despite the fact that she has a brother suffering from hearing loss triggered by an allelic GJB2 c.176 del 16 mutation.We cloned the GJB2 genes derived from their respective blood genomic DNA into GFP fused plasmids and transfected those plasmids into the 293 T cell line to test for gene function.While the mutated GJB2gene(GJB2 c.176 del 16) of her deaf brother was found to be unable to form the gap junction structure between two adjacent cells,the baby girl’s GJB2 gene ran into no such problems.Conclusion:The screening and sequencing as well as the GJB2 gene function tests invariably showed results consistent with the ABR tested hearing phenotype,which means that the child,with a normal wild type GJB2 gene,does not need early intervention to prevent her from developing hearing loss and dysphonia at a later stage in life.展开更多
文摘Objective:To identify potential key genes associated with pre-eclampsia through bioinformatics analysis,construct predictive models using machine-learning algorithms,and evaluate the models'performance in predicting pre-eclampsia.Methods:Gene-expression microarray datasets GSE10588,GSE66273,and GSE30186 related to pre-eclampsia were downloaded from the gene expression omnibus(GEO).Data were normalized using R,and differentially expressed genes(DEGs)were identified.LASSO regression was applied to further filter DEGs.Based on the selected DEGs,six machine-learning models-logistic regression(LR),random forest(RF),support vector machine(SVM),K-nearest neighbors(KNN),neural network(NN),and eXtreme gradient boosting(XGBoost)were built in R,and their performance was validated.Results:From the three datasets,a total of 1,363 genes were extracted.LASSO regression narrowed these to 265 candidate key genes.Multivariate analysis ultimately identified four genes closely associated with pre-eclampsia:EVI5,GCLM,LEP,and SYNPO2L.Using these four key genes,six machine-learning models were constructed.Receiver operating characteristic(ROC)analysis showed that all models achieved AUC>0.9:LR(AUC=0.983,95%CI=0.942-0.998),RF(AUC=0.961,95%CI=0.912-0.987),SVM(AUC=0.936,95%CI=0.879-0.972),KNN(AUC=0.970,95%CI=0.924-0.992),NN(AUC=0.916,95%CI=0.854-0.958),and XGBoost(AUC=0.952,95%CI=0.900-0.982).There was no statistically significant difference among the AUCs of the models(P>0.05).Conclusion:This study identified four key genes linked to preeclampsia through integrated bioinformatics analysis.Predictive models built on these genes can accurately forecast the occurrence of pre-eclampsia,suggesting that the four genes may serve as potential biomarkers for early diagnosis and therapeutic targeting of pre-eclampsia.
基金supported by grants from the Hi-Tech Research and Development Program of China (No.2012AA06A302)the Strategic Priority Research Program of the Chinese Academy of Sciences (Nos.XDB14040102, YSW2013A01)the National Natural Science Foundation of China (No.21377153)
文摘Amphibian metamorphosis provides a wonderful model to study the thyroid hormone（TH）signaling disrupting activity of environmental chemicals, with Xenopus laevis as the most commonly used species. This study aimed to establish a rapid and sensitive screening assay based on TH-response gene expression analysis using Pelophylax nigromaculatus, a native frog species distributed widely in East Asia, especially in China. To achieve this, five candidate TH-response genes that were sensitive to T3 induction were chosen as molecular markers, and T3 induction was determined as 0.2 nmol/L T3 exposure for 48 hr. The developed assay can detect the agonistic activity of T3 with a lowest observed effective concentration of 0.001 nmol/L and EC50 at around 0.118–1.229 nmol/L, exhibiting comparable or higher sensitivity than previously reported assays. We further validated the efficiency of the developed assay by detecting the TH signaling disrupting activity of tetrabromobisphenol A（TBBPA）, a known TH signaling disruptor. In accordance with previous reports, we found a weak TH agonistic activity for TBBPA in the absence of T3,whereas a TH antagonistic activity was found for TBBPA at higher concentrations in the presence of T3, showing that the P. nigromaculatus assay is effective for detecting TH signaling disrupting activity. Importantly, we observed non-monotonic dose-dependent disrupting activity of TBBPA in the presence of T3, which is difficult to detect with in vitro reporter gene assays. Overall, the developed P. nigromaculatus assay can be used to screen TH signaling disrupting activity of environmental chemicals with high sensitivity.
文摘Screening gene function in vivo is a powerful approach to discover novel drug targets. We present high-throughput screening （HTS） data for 3 762 distinct global gene knockout （KO） mouse lines with viable adult homozygous mice generated using either gene-trap or homologous recombination technologies. Bone mass was determined from DEXA scans of male and female mice at 14 weeks of age and by microCT analyses of bones from male mice at 16 weeks of age. Wild-type （WT） cagemates/littermates were examined for each gene KO. Lethality was observed in an additional 850 KO lines. Since primary HTS are susceptible to false positive findings, additional cohorts of mice from KO lines with intriguing HTS bone data were examined. Aging, ovariectomy, histomorphometry and bone strength studies were performed and possible non-skeletal phenotypes were explored. Together, these screens identified multiple genes affecting bone mass： 23 previously reported genes （Calcr, Cebpb, Crtap, Dcstamp, Dkkl, Duoxa2, Enppl, Fgf23, Kissl/Kisslr, Kl （Klotho）, Lrp5, Mstn, Neol, Npr2, Ostml, Postn, Sfrp4, S1c30a5, Sic39a13, Sost, Sumf1, Src, Wnt10b）, five novel genes extensively characterized （Cldn18, Fam20c, Lrrkl, Sgpll, Wnt16）, five novel genes with preliminary characterization （Agpat2, RassfS, Slc10a7, Stc26a7, Slc30a10） and three novel undisclosed genes coding for potential osteoporosis drug targets.
基金supported by the National Natural Science Foundation of China(81101302,31270185)SKLID Development Grant(2014,SKLID201)
文摘Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking and gait. This disease can not be clearly identified through laboratory tests at present, thus application of high-throughput technique in studying the expression profiles of PD helps to find the genetic markers for its early diagnosis. Studies on expression profiles of neurodegenerative diseases have revealed the novel genes and pathways involved in the progress of illness. In this study, the expression profiles of PD in blood were compared, showing that 181 differentially expressed genes （DEG） exhibit a similar expression trend both in patients and in normal controls.
基金financially supported by the National Basic Research Program of China(973 Program)(No.2009CB918702)the National Natural Science Foundation of China(Nos.31071087 and 31100889)
文摘F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 out of 75 F-box proteins have experimentally documented substrates, whereas in Drosophila 12 F-box proteins have been characterized with known substrates. To systematically investigate the genetic and molecular functions of F-box proteins in Drosophila, we performed a survey of the literature and databases. We identified 45 Drosophila genes that encode proteins containing at least one F-box domain. We collected publically available RNAi lines against these genes and used them in a tissue-specific RNAi-based phenotypic screen. Here, we present our systematic phenotypic dataset from the eye, the wing and the notum. This dataset is the first of its kind and represents a useful resource for future studies of the molecular and genetic functions of F-box genes in Drosophila. Our results show that, as expected, F-box genes in Drosophila have regulatory roles in a diverse array of processes including cell proliferation, cell growth, signal transduction, and cellular and animal survival.
基金supported by the Industry Research Special Foundation of China Ministry of Health(No.201202021)
文摘Yersinia pestis is the causative agent of bubonic and pneumonic plagues. Strains of Y. pestis are classified into four biovars： antiqua, mediaevalis, orientalis, and microtus[11. There are two microtus-related plague loci in China： the Microtus brandti plague focus in the Xilin Gol Grassland （focus L） and the Microtus fuscus plague focus in the Ojnghai-Tibet Plateau （focus M）.
文摘Prenatal diagnosis was requested for an undiagnosed eye disease showing X-linked inheritance in a family. No medical records existed for the affected family members..Mapping of the X chromosome and candidate gene mutation screening identified a c.C267A[p.F89L] mutation in NPD previously described as possibly causing Norrie disease..The detection of the c.C267A[p.F89L] variant in another unrelated family confirms the pathogenic nature of the mutation for the Norrie disease phenotype. Gene mapping, haplotype analysis, and candidate gene screening have been previously utilized in research applications but were applied here in a diagnostic setting due to the scarcity of available clinical information..The clinical diagnosis and mutation identification were critical for providing proper genetic counseling and prenatal diagnosis for this family.
文摘Purpose: To compare the sensitivity of Hexosaminidase A (HexA) enzyme-based testing to gene sequencing for carrier detection in non-Jewish individuals. Methods: Blood samples were obtained from parents and relatives of affected patients at an annual Tay-Sachs and Allied Diseases Foundation meeting. A family history was taken for each individual. Samples were analyzed for leukocyte HexA activity, serum HexA activity and subjected to extensive gene sequencing. The results from these analyses were combined with our previously published data describing 34 obligate Tay-Sachs disease (TSD) carriers. Results: Twelve additional TSD carriers were detected in this study. Gene sequencing successfully identified all 12 carriers whereas enzyme analysis identified 11 of 12 carriers. This individual is a carrier of the B1 variant that is known to cause false negative results with enzyme testing. Combined data from 46 non-Jewish TSD carriers revealed that gene sequencing had a higher sensitivity rate than HexA enzyme-based testing (94% versus 87%) in non-Jewish TSD carriers. In our series, approximately 4% of non-Jewish TSD carriers have this mutation. Conclusions: HexA gene sequencing provides a higher sensitivity for TSD carrier detection than HexA based enzyme analysis in non-Jewish patients primarily due to the presence of individuals with the B1 variant.
文摘Aim: To assess the clinical significance of hTERC amplification for cervical cancer screening detected by fluorescence in situ hybridization (FISH) and compare it with that of current screening methods within the same group. Methods: A total of one hundred and nine women were recruited in this study. All of them had liquid-based thin-prep cytologic test (TCT), human papillomavirus (HPV) DNA testing and hTERC gene amplification analysis using interphase two-color FISH. In addition, colposcopically directed biopsy and/or cone biopsy were conducted for definite histopathologic diagnosis for each case. The optimal threashold of hTERC gene amplification by fluorescence in situ hybridization (FISH) were assecced by receiver operating characteristic (ROC) curve. The results of hTERC gene amplification analysis were compared with the cytological analysis, HPV DNA testing and those of subsequent biopsies. Results: Among the 109 patients, 18 were benign lesion, 17 were LSIL, 66 were HSIL and 8 were invasive carcinoma of cervix (ICC). Of them, hTERC-positive cases were found in 0.0% (0/18) of normal specimens, 11.8% (2/17) of LSIL, 72.7% (48/66) of HSIL and 100.0% (8/8) of ICC, respectively. The positive rate of hTERC gene amplification was significantly higher in HSIL and ICC compared with normal and LSIL (all P < 0.01).The optimal cut-off point of percentages of cells with hTERC amplification was determined as 5.5%. Using this threshold the hTERC test reached a much higher specificity(94.3%, 33/35) and a relatively lower sensitivity(77.0%, 57/74) to distinguish benign lesion and LSIL from HSIL and ICC in comparison with HR-HPV test (51.4%;91.9%) and TCT (74.3%;81.1%). Area Under the Curve revealed that hTERC amplification test performed more accurately (area under the curve = 0.857) compared to HPV test (area under the curve = 0.717) and cytology(area under the curve = 0.777) to discriminate HSIL or higher from LSIL or lower. This study also found a significant positive correlation between positive hTERC gain and HR-HPV infection, abnormal cytological or histopathologic lesions (all P < 0.01) in patients with cervical diseases. Conclusion: hTERC amplification testing may be a promising adjunct to screen women for cervical precancer or cancer with high specificity and accuracy.
文摘Wolman disease is a rare autosomal recessive disorder caused by mutations in the LIPA gene (10q23.31). The LIPA gene encodes lysosomal acid lipase (LAL), which plays a key role in hydrolysis of the cholesteryl esters and triglycerides. Two unrelated families from Bulgaria were referred for genetic testing with clinical diagnosis Wolman disease. Sanger sequencing of all coding exons and exon-intron boundaries of the LIPA gene was performed. The index patients were found to be homozygous for two different mutations in the LIPA gene: a missense mutation, c.260G > T, p.Gly87Val, which affects the enzyme active site and a splice-site change, c.822+1G > A, which most probably destroys the enzyme polypeptide chain. These two completely different types of mutations along the LIPA gene resulted in a very similar phenotype involving liver, kidney, gastrointestinal, muscle and blood disturbances. As consanguinity is not typical for the Bulgarian population, a possible explanation of the homozygosity could be presence of endemic regions for given mutations. To check this hypothesis, selective screening for these mutations was performed in two presumable endemic regions in Bulgaria. Altogether, 100 newborns were screened for p.Gly87Val mutation and the detected carrier frequency was about 1% (1/100), while in the group of 100 newborns screened for the c.822 + 1G > A mutation the detected carrier frequency was 2% (2/100). The results indicate a high recurrence risk of Wolman disease in these particular Bulgarian regions of about 1:10000. These findings are from crucial importance for the inhabitants of the corresponding parts of Bulgaria. They may benefit from early genetic testing and adequate genetic counselling during family planning.
文摘以高耐热性玉米品种郑单958、低耐热性玉米品种先玉335为试验材料,以正常生长条件为对照(CK),利用半自动伸缩高温棚进行花期高温胁迫(HT)处理,通过circRNA高通量测序筛选高温胁迫下不同玉米品种花粉中差异表达的环状RNA(circRNA),对其来源基因进行GO和KEGG富集分析,并筛选具有miRNA结合位点的差异表达circRNA,预测其下游目的基因,分析玉米花粉中响应高温胁迫的潜在circRNA-miRNA-mRNA共表达调控网络,从多层面解析玉米花粉中调控高温胁迫的分子作用机制,为提高玉米品种的耐热性提供理论依据。结果表明,在郑单958、先玉335不同样本中共鉴定出1 843个不同的circRNA,它们在玉米染色体中的分布不同。每个circRNA所包含的外显子数目也不相同,其中,大多数(624个)circRNA只含有1个外显子。在郑单958花粉中共鉴定出1 563个circRNA,其中,CK958-1、CK958-2、CK958-3中分别鉴定出305、213、356个circRNA,HT958-1、HT958-2、HT958-3中分别鉴定出222、242、225个circRNA。在先玉335花粉中共鉴定出1 423个circRNA,其中,CK335-1、CK335-2、CK335-3中分别鉴定出272、188、229个circRNA,HT335-1、HT335-2、HT335-3中分别鉴定出259、237、238个circRNA。不同样本中占比最高的均为外显子circRNA。circRNA与其来源基因不是一一对应的关系,有748个circRNA来源基因通过反向剪接机制只形成1个circRNA,156个circRNA来源基因通过反向剪接机制各自形成2个circRNA。在郑单958高温胁迫花粉与对照花粉对比组(HT958 vs CK958)中共筛选到9个差异表达circRNA,其中2个circRNA呈上调表达,其来源基因显著富集到焦磷酸酶活性、核苷酸磷酸代谢过程、糖基磷脂酰肌醇(GPI)锚定代谢过程等17个GO条目,显著富集到GPI锚定生物合成、代谢途径等KEGG通路。在先玉335高温胁迫花粉与对照花粉对比组(HT335 vs CK335)中共筛选到1个差异表达circRNA,其来源基因没有显著富集到任何GO条目、KEGG通路。在郑单958高温胁迫花粉与先玉335高温胁迫花粉对比组(HT958 vs HT335)中共筛选到17个差异表达circRNA,其中6个circRNA呈上调表达,其来源基因显著富集到内质网系统、高尔基相关囊泡膜、膜蛋白水解等16个GO条目中,没有显著富集到任何KEGG代谢通路。5个circRNA具有miRNA结合位点,可以作为海绵岛吸附miRNA间接调控下游靶标基因的表达,构建了包括5个circRNA、5个不同家族miRNA、2个mRNA在内的circRNA-miRNA-mRNA共表达调控网络。筛选到了54个circRNA包含内部核糖体进入位点(IRES),可以翻译表达多肽或者蛋白质直接作用于靶标基因。
基金supported by the Research Fund of the Istanbul University, Turkey (No. 480 [2359/2006])
文摘Moebius syndrome is a rare disorder primarily characterized by congenital facial palsy, frequently accompanied by ocular abduction anomalies and occasionally associated with orofacial, limb and musculoskeletal malformations. Abnormal development of cranial nerves Ⅴ through Ⅻ underlines the disease pathogenesis. Although a genetic etiology for Moebius syndrome was proposed, molecular genetic studies to identify the causative gene（s） are scarce. In this study, we selected two candidate genes. One is BASP1 residing in a human chromosome 5p15.1-p15.2, syntenic to mouse chromosome 15qA2-qB2, to which a mouse model with facial nerve anomalies was mapped. The other is transcribed processed pseudogene TPψg-BASP1, which is located on chromosome 13q flanking the putative locus for Moebius syndrome and might be involved in the regulation of the transcripts encoded by BASP1. Mutation analyses in nineteen patients excluded these genes as being candidates for Moebius syndrome.
基金supported by grants from National Natural Science Foundation of China (81470684)Clinical Special Fund of Jiangsu Province (b12014032)+4 种基金Postdoctoral Science Foundation of China (2015M571818)Six Major Categories Talent (2014-WSN-043,2011-WS-074)Innovation and Entrepreneurship Training Program for College Students in Jiangsu Province (201510313003Z,201510313003,KYLX14-1455)Clinic Medical Special Foundation of Jiangsu Province (b12014032)Project of natural science research area of Jiangsu Province (16KJB320016)
文摘Objective:To determine whether a new-born child from a family carrying a deafness gene needs cochlear implantation to avoid dysphonia by screening and sequencing a deafness-related gene.Results:Both screening and sequencing results confirmed that the new born child had a normal GJB2 gene despite the fact that she has a brother suffering from hearing loss triggered by an allelic GJB2 c.176 del 16 mutation.We cloned the GJB2 genes derived from their respective blood genomic DNA into GFP fused plasmids and transfected those plasmids into the 293 T cell line to test for gene function.While the mutated GJB2gene(GJB2 c.176 del 16) of her deaf brother was found to be unable to form the gap junction structure between two adjacent cells,the baby girl’s GJB2 gene ran into no such problems.Conclusion:The screening and sequencing as well as the GJB2 gene function tests invariably showed results consistent with the ABR tested hearing phenotype,which means that the child,with a normal wild type GJB2 gene,does not need early intervention to prevent her from developing hearing loss and dysphonia at a later stage in life.
