AIM:To investigate the stability of the seven housekeeping genes:beta-actin(ActB),glyceraldehyde-3-phosphate dehydrogenase(GAPDH),18s ribosomal unit 5(18s),cyclophilin A(CycA),hypoxanthine-guanine phosphoribosyl trans...AIM:To investigate the stability of the seven housekeeping genes:beta-actin(ActB),glyceraldehyde-3-phosphate dehydrogenase(GAPDH),18s ribosomal unit 5(18s),cyclophilin A(CycA),hypoxanthine-guanine phosphoribosyl transferase(HPRT),ribosomal protein large P0(36B4)and terminal uridylyl transferase 1(U6)in the diabetic retinal tissue of rat model.METHODS:The expression of these seven genes in rat retinal tissues was determined using real-time quantitative reverse transcription polymerase chain reaction(RT-qPCR)in two groups;normal control rats and streptozotocininduced diabetic rats.The stability analysis of gene expression was investigated using geNorm,NormFinder,BestKeeper,and comparative delta-Ct(ΔCt)algorithms.RESULTS:The 36B4 gene was stably expressed in the retinal tissues of normal control animals;however,it was less stable in diabetic retinas.The 18s gene was expressed consistently in both normal control and diabetic rats’retinal tissue.That this gene was the best reference for data normalisation in RT-qPCR studies that used the retinal tissue of streptozotocin-induced diabetic rats.Furthermore,there was no ideal gene stably expressed for use in all experimental settings.CONCLUSION:Identifying relevant genes is a need for achieving RT-qPCR validity and reliability and must be appropriately achieved based on a specific experimental setting.展开更多
The response of transcription factor genes to low nitrogen stress was studied to provide molecular basis for improving the absorption and utilization efficiency of nitrogen fertilizer in rice. The agilent rice genome ...The response of transcription factor genes to low nitrogen stress was studied to provide molecular basis for improving the absorption and utilization efficiency of nitrogen fertilizer in rice. The agilent rice genome arrays were used to study the varied expression of transcription factor genes in two rice varieties (SN 196 and Toyonishhiki) with different chlorophyll contents under low nitrogen stress. The results showed that a total of 53 transcription factor genes (35 down-regulated and 18 up-regulated genes at the transcription level) in flag leaves of super-green rice SN196 and 27 transcription factor genes (21 down-regulated and 6 up-regulated genes at the transcription level) in flag leaves of Toyonishiki were affected by low nitrogen stress. Among those nitrogen-responsive genes, 48 transcription factor genes in SN196 and 22 in Toyonishiki were variety-specific. There were overlapped transcription factor genes responded to low nitrogen stress between SN196 and Toyonishiki, with 1 up-regulated and 4 down-regulated at the transcription level. Distributions of low nitrogen responsive genes on chromosomes were different in two rice varieties.展开更多
Portunus trituberculatus is an ide al model for elucidating crustacean genetic networks.Here we combined single molecule real-time(SMRT)sequencing and Illumina RNA-seq to characterize the coding genes,non-coding RNAs ...Portunus trituberculatus is an ide al model for elucidating crustacean genetic networks.Here we combined single molecule real-time(SMRT)sequencing and Illumina RNA-seq to characterize the coding genes,non-coding RNAs and pseudogenes and further to improve the genome annotation information of P.tritub erculatus.In this study,we assembled 9694 non-redundancy full-length transcripts,and 658737307-bp repetitive sequences were identified in the P.trituberculatus full-length transcriptome.We also predicted the P.tritub erculatus genome structure based on full-length transcripts,including 18602 genes,28686 non-coding RNAs,1407 pseudogenes,740 motif,and 26434 domain.Meanwhile,14460,10211,5412,7314,and 14448 genes had significant matches with sequences in the NR,KOG,GO,KEGG,and TrEMBL database,respectively.Overall,our work firstly provided the long-read transcriptome and we believed that these data are very necessary to improve the annotation information of P.trituberculatus genome structure,and useful information for the future studies on evolution and physiological regulation of P.trituberculatus.展开更多
The sheep genome harbours approximately 20 copies of endogenous beta-retroviruses (enJSRVs), and circumstantial evidence suggests that enJSRVs might play a role in mammalian reproduction, particularly placental morp...The sheep genome harbours approximately 20 copies of endogenous beta-retroviruses (enJSRVs), and circumstantial evidence suggests that enJSRVs might play a role in mammalian reproduction, particularly placental morphogenesis. This study was aimed to assess the expression of mRNAs of an enJSRV and its receptor, HYAL2, in the uterus and conceptuses of Mongolian ewes throughout gestation, using real-time reverse transcription polymerase chain reaction and in situ hybridization analysis. The results showed that enJSRV and HYAL2 mRNAs were found to be expressed throughout gestation in the endometrium, chorion, placenta, and conceptus. The enJSRV mRNA was most abundant in the placenta on day 90 of pregnancy, in the endometrium on day 30 and 50, and in the chorion on day 70 and 110. However, HYAL2 mRNA was most abundant in the endometrium on day 30. These differences were all significantly different from each other (P〈0.01). In situ hybridization showed that enJSRV and HYAL2 mRNAs were specifically expressed in endometrial luminal epithelium and glandular epithelium, trophoblastic giant binucleated cells (BNCs), endometrial caruncles, placental cotyledons, stroma, trophectoderm, as well as multinucleated syncytia of the placenta and blood vessel endothelial cells. Collectively, little is known about the molecular mechanisms by which trophoblastic differentiation and multinucleated syncytia formation are regulated by enJSRVs. However, the temporal and spatial distributions of enJSRV expression in the uterus and conceptus indicate that differentiation of BNCs and the formation of a multinucleated syncytiotrophoblast involve enJSRV and possibly its cellular receptor, HYAL2. Therefore, enJSRV and HYAL2 appear to play important roles in the female reproductive physiology in this breed of sheep.展开更多
Drought is one of the major abiotic stresses which adversely affect crop plants limiting growth and yield potential.Structural and functional characterization of drought stress-induced genes has contributed to a bette...Drought is one of the major abiotic stresses which adversely affect crop plants limiting growth and yield potential.Structural and functional characterization of drought stress-induced genes has contributed to a better understanding of how plants respond and adapt to the drought stress.In the present study,differential display technique was employed to study the gene expression of rice plants at the reproductive stage that were subjected to drought stress by withholding water,Pseudomonas fluorescens strain(Pf1) treated plants subjected for drought stress by withholding water and control(well-watered).Differentially expressed c DNAs of six genes(COX1,PKDP,b ZIP1,AP2-EREBP,Hsp20 and COC1) were identified,cloned and sequenced.Real-time q PCR analysis showed that all the six genes were upregulated in drought-stressed plants treated with Pf1.This revealed that the remarkable influence of Pf1 colonization leads to drought tolerance at the reproductive stage.These results showed that high levels of gene expression in plants lacking adequate water can be remarkably influenced by Pf1 colonization,which might be a key element for induced systemic tolerance by microbes.展开更多
Old astrocyte specifically induced substance (OASIS) is an endoplasmic reticulum (ER) stress transducer specifically expressed in astrocytes and osteoblasts. OASIS regulates the differentiation of neural precursor...Old astrocyte specifically induced substance (OASIS) is an endoplasmic reticulum (ER) stress transducer specifically expressed in astrocytes and osteoblasts. OASIS regulates the differentiation of neural precursor cells into astrocytes in the central nervous system. This study aimed to elucidate the involvement of ER stress responses stimulated via OASIS in astrogliosis following spinal cord injury. In a mouse model of spinal cord contusion injury, OASIS mRNA and protein expression were evaluated at days 7 and 14. A significant increase in OASIS mRNA on day 7 and an increase in protein on days 7 and 14 was observed in injured spinal cords. Immunostaining on day 7 revealed co-localization of OASIS and astrocytes in the periphery of the injury site. Furthermore, anti-OASIS small interfering RNA (siRNA) was injected at the injury sites on day 5 to elucidate the function of OASIS. Treatment with anti-OASIS siRNA caused a significant decrease in OASIS mRNA on day 7 and protein on days 7 and 14, and was associated with the inhibition of astrogliosis and hindlimb motor function recovery. Results of our study show that OASIS expression synchronizes with astrogliosis and is functionally associated with astrogliosis after spinal cord injury.展开更多
In this paper we propose simple enhancements to the bandwidth (BW) request messages in IEEE 802.16 for supporting real-time packet voice traffic. Three different BW request formats are proposed, each requiring a dif...In this paper we propose simple enhancements to the bandwidth (BW) request messages in IEEE 802.16 for supporting real-time packet voice traffic. Three different BW request formats are proposed, each requiring a different amount of latency information about the buffered packets at the SS. On this basis, packet scheduling schemes are proposed for the BS to make resource allocations for real-time traffic. Our results show that the proposed BW request and scheduling schemes achieve significantly lower packet loss probability than the standard IEEE 802.16 BW request with round robin scheduling. The results further show that there is an optimum point about how much delay information the SS should report to the BS in order to best utilize the uplink resources while the SS provides satisfactory real-time performance for the voice traffic.展开更多
Stem cells were isolated from human dental pulp using an optimized method, in which pulp pieces were digested by enzymes and immobilized to enhance cell outgrowth. Stem cell marker expression was detected by reverse t...Stem cells were isolated from human dental pulp using an optimized method, in which pulp pieces were digested by enzymes and immobilized to enhance cell outgrowth. Stem cell marker expression was detected by reverse transcription-PCR (RT-PCR), and differentiation markers were detected by real-time quantitative RT-PCR and immunocytochemistry. Results showed that dental pulp stem cells actively expressed nanog, oct4, nucleostemin slain-l, jmjdla, jmjd2c, and cyclin DI. When stem cells were induced to differentiate into neurons, nucleostemin, nanog, and cyclin D1 expression significantly decreased, whereas expression of neuronal markers, such as microtubule associated protein-2 and neurofilament-heavy, significantly increased. These results suggested that stem cells exited a pluripotent state and entered a neuronal differentiation pathway. In addition, results demonstrated that human dental pulp serves as a reservoir of stem cells that express defined stem cell markers; these cells were easily isolated and were induced to differentiate towards a desired cell lineage.展开更多
Metabolizing enzymes play important roles in the detoxification of various pollutants in aquatic organisms, thereby they can also be used to provide early-warning signals of environmental risks. Real-time quantitative...Metabolizing enzymes play important roles in the detoxification of various pollutants in aquatic organisms, thereby they can also be used to provide early-warning signals of environmental risks. Real-time quantitative reverse-transcription polymerase chain reaction assays were developed to quantify cytochrome P450 1A (CYP1A), superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase (CAT), and glutathione-S-transferase (GST) in crucian carp (Carassius auratus). The methods were then used to detect the respective mRNA expression levels in liver tissue in wild crucian carp from the Hun River, North China. CYP1A mRNA expression was significantly up-regulated in fish from stations $5, $6, and $8 (p 〈 0.05). SOD mRNA expression was significantly down-regulated in downstream areas relative to fish from upstream sites (p 〈 0.05); GPx and CAT mRNA expression levels were also down-regulated at $9 (p 〈 0.05). In contrast, GST mRNA expression showed no obvious change between fish collected from up- or downstream areas of the river. Finally, an integrated biomarker response was used to evaluate the integrated impact of pollutants in the Hun River and allow better comprehension of the real toxicological risk of these investigated sites.展开更多
The technique of SYBR Green-based quantitative real-time reverse transcription polymerase chain reaction(real-time RT-PCR)was applied to quantitative detect a 764 bp nucleotide sequence containing total coat protein(c...The technique of SYBR Green-based quantitative real-time reverse transcription polymerase chain reaction(real-time RT-PCR)was applied to quantitative detect a 764 bp nucleotide sequence containing total coat protein(cp)gene of Cymbidium mosaic virus(CyMV).The plasmid containing the target sequence was constructed to prepare the standard curve and detect the sensitivity.The standard curve was drawn based on the linear relationship between the logarithm(base 10)of the quantity of target sequence and cycle threshold[C(T)].While the concentration of plasmid DNA falling within the range of 2.6×10^(7)to 2.6×10^(2)copies per tube established a regression equation,y=-0.3583x+10.32,and related coefficient:r^(2)=0.995.The real-time RT-PCR assay for CyMV had a minimum detectable quantity of two copies per tube.The naturally infected samples of Phalaenopsis sp.and the artificially inoculated samples of Arachnis sp.with trace CyMV were quantitatively detected using this method.CyMVin the positive samples of Phalaenopsis sp.and Arachnis sp.was confirmed by DNA sequencing and cp gene homeology blast.The results showed that CyMV extracted from the leaves of orchid in Hangzhou,Zhejiang Province,China,could be derived from Kunming city(KM),Yunnan Province,China.This method characterized by high sensitivity,specificity,and precision is suitable for early diagnosis and quantitative detection of CyMV.展开更多
基金Supported by grant from Fundamental Research Grant Scheme by Ministry of Higher Education(MoHE)600-IRMI/FRGS 5/3(101/2019).
文摘AIM:To investigate the stability of the seven housekeeping genes:beta-actin(ActB),glyceraldehyde-3-phosphate dehydrogenase(GAPDH),18s ribosomal unit 5(18s),cyclophilin A(CycA),hypoxanthine-guanine phosphoribosyl transferase(HPRT),ribosomal protein large P0(36B4)and terminal uridylyl transferase 1(U6)in the diabetic retinal tissue of rat model.METHODS:The expression of these seven genes in rat retinal tissues was determined using real-time quantitative reverse transcription polymerase chain reaction(RT-qPCR)in two groups;normal control rats and streptozotocininduced diabetic rats.The stability analysis of gene expression was investigated using geNorm,NormFinder,BestKeeper,and comparative delta-Ct(ΔCt)algorithms.RESULTS:The 36B4 gene was stably expressed in the retinal tissues of normal control animals;however,it was less stable in diabetic retinas.The 18s gene was expressed consistently in both normal control and diabetic rats’retinal tissue.That this gene was the best reference for data normalisation in RT-qPCR studies that used the retinal tissue of streptozotocin-induced diabetic rats.Furthermore,there was no ideal gene stably expressed for use in all experimental settings.CONCLUSION:Identifying relevant genes is a need for achieving RT-qPCR validity and reliability and must be appropriately achieved based on a specific experimental setting.
基金supported by the Agricultural Science and Technology Achievement Transformation Fund of Science and Technology Ministry of China(Grant No. 2010GB2B000077)the Special Fund forAgro-scientific Research in the Public Interest of theministry of Agriculture of China (Grant No.201203026)
文摘The response of transcription factor genes to low nitrogen stress was studied to provide molecular basis for improving the absorption and utilization efficiency of nitrogen fertilizer in rice. The agilent rice genome arrays were used to study the varied expression of transcription factor genes in two rice varieties (SN 196 and Toyonishhiki) with different chlorophyll contents under low nitrogen stress. The results showed that a total of 53 transcription factor genes (35 down-regulated and 18 up-regulated genes at the transcription level) in flag leaves of super-green rice SN196 and 27 transcription factor genes (21 down-regulated and 6 up-regulated genes at the transcription level) in flag leaves of Toyonishiki were affected by low nitrogen stress. Among those nitrogen-responsive genes, 48 transcription factor genes in SN196 and 22 in Toyonishiki were variety-specific. There were overlapped transcription factor genes responded to low nitrogen stress between SN196 and Toyonishiki, with 1 up-regulated and 4 down-regulated at the transcription level. Distributions of low nitrogen responsive genes on chromosomes were different in two rice varieties.
基金Supported by the National Key Research and Development Program of China(No.2017YFA0604904)the Zhejiang Provincial Natural Science Foundation of China(No.LR21D060003)。
文摘Portunus trituberculatus is an ide al model for elucidating crustacean genetic networks.Here we combined single molecule real-time(SMRT)sequencing and Illumina RNA-seq to characterize the coding genes,non-coding RNAs and pseudogenes and further to improve the genome annotation information of P.tritub erculatus.In this study,we assembled 9694 non-redundancy full-length transcripts,and 658737307-bp repetitive sequences were identified in the P.trituberculatus full-length transcriptome.We also predicted the P.tritub erculatus genome structure based on full-length transcripts,including 18602 genes,28686 non-coding RNAs,1407 pseudogenes,740 motif,and 26434 domain.Meanwhile,14460,10211,5412,7314,and 14448 genes had significant matches with sequences in the NR,KOG,GO,KEGG,and TrEMBL database,respectively.Overall,our work firstly provided the long-read transcriptome and we believed that these data are very necessary to improve the annotation information of P.trituberculatus genome structure,and useful information for the future studies on evolution and physiological regulation of P.trituberculatus.
基金funded by the National Natural Science Foundation of China (30960271 and 31160493)the doctor fund project of Ministry of Education of China(20111515110008)
文摘The sheep genome harbours approximately 20 copies of endogenous beta-retroviruses (enJSRVs), and circumstantial evidence suggests that enJSRVs might play a role in mammalian reproduction, particularly placental morphogenesis. This study was aimed to assess the expression of mRNAs of an enJSRV and its receptor, HYAL2, in the uterus and conceptuses of Mongolian ewes throughout gestation, using real-time reverse transcription polymerase chain reaction and in situ hybridization analysis. The results showed that enJSRV and HYAL2 mRNAs were found to be expressed throughout gestation in the endometrium, chorion, placenta, and conceptus. The enJSRV mRNA was most abundant in the placenta on day 90 of pregnancy, in the endometrium on day 30 and 50, and in the chorion on day 70 and 110. However, HYAL2 mRNA was most abundant in the endometrium on day 30. These differences were all significantly different from each other (P〈0.01). In situ hybridization showed that enJSRV and HYAL2 mRNAs were specifically expressed in endometrial luminal epithelium and glandular epithelium, trophoblastic giant binucleated cells (BNCs), endometrial caruncles, placental cotyledons, stroma, trophectoderm, as well as multinucleated syncytia of the placenta and blood vessel endothelial cells. Collectively, little is known about the molecular mechanisms by which trophoblastic differentiation and multinucleated syncytia formation are regulated by enJSRVs. However, the temporal and spatial distributions of enJSRV expression in the uterus and conceptus indicate that differentiation of BNCs and the formation of a multinucleated syncytiotrophoblast involve enJSRV and possibly its cellular receptor, HYAL2. Therefore, enJSRV and HYAL2 appear to play important roles in the female reproductive physiology in this breed of sheep.
基金the Jawaharlal Nehru University(JNU) research fellowship sponsored by the Department of Biotechnology(DBT),Government of India
文摘Drought is one of the major abiotic stresses which adversely affect crop plants limiting growth and yield potential.Structural and functional characterization of drought stress-induced genes has contributed to a better understanding of how plants respond and adapt to the drought stress.In the present study,differential display technique was employed to study the gene expression of rice plants at the reproductive stage that were subjected to drought stress by withholding water,Pseudomonas fluorescens strain(Pf1) treated plants subjected for drought stress by withholding water and control(well-watered).Differentially expressed c DNAs of six genes(COX1,PKDP,b ZIP1,AP2-EREBP,Hsp20 and COC1) were identified,cloned and sequenced.Real-time q PCR analysis showed that all the six genes were upregulated in drought-stressed plants treated with Pf1.This revealed that the remarkable influence of Pf1 colonization leads to drought tolerance at the reproductive stage.These results showed that high levels of gene expression in plants lacking adequate water can be remarkably influenced by Pf1 colonization,which might be a key element for induced systemic tolerance by microbes.
基金supported by MEXT/JSPS KAKENHI Grant-in-Aid for Scientific Research(C)to NK(Grant No.17K10931)
文摘Old astrocyte specifically induced substance (OASIS) is an endoplasmic reticulum (ER) stress transducer specifically expressed in astrocytes and osteoblasts. OASIS regulates the differentiation of neural precursor cells into astrocytes in the central nervous system. This study aimed to elucidate the involvement of ER stress responses stimulated via OASIS in astrogliosis following spinal cord injury. In a mouse model of spinal cord contusion injury, OASIS mRNA and protein expression were evaluated at days 7 and 14. A significant increase in OASIS mRNA on day 7 and an increase in protein on days 7 and 14 was observed in injured spinal cords. Immunostaining on day 7 revealed co-localization of OASIS and astrocytes in the periphery of the injury site. Furthermore, anti-OASIS small interfering RNA (siRNA) was injected at the injury sites on day 5 to elucidate the function of OASIS. Treatment with anti-OASIS siRNA caused a significant decrease in OASIS mRNA on day 7 and protein on days 7 and 14, and was associated with the inhibition of astrogliosis and hindlimb motor function recovery. Results of our study show that OASIS expression synchronizes with astrogliosis and is functionally associated with astrogliosis after spinal cord injury.
基金supported by Natural Sciences and Engineering Research Council of Canada under Grant No. 5-43990.
文摘In this paper we propose simple enhancements to the bandwidth (BW) request messages in IEEE 802.16 for supporting real-time packet voice traffic. Three different BW request formats are proposed, each requiring a different amount of latency information about the buffered packets at the SS. On this basis, packet scheduling schemes are proposed for the BS to make resource allocations for real-time traffic. Our results show that the proposed BW request and scheduling schemes achieve significantly lower packet loss probability than the standard IEEE 802.16 BW request with round robin scheduling. The results further show that there is an optimum point about how much delay information the SS should report to the BS in order to best utilize the uplink resources while the SS provides satisfactory real-time performance for the voice traffic.
基金the research grant No. 1.1266 from International Centre for Science, High Technology and Environmental Sciences
文摘Stem cells were isolated from human dental pulp using an optimized method, in which pulp pieces were digested by enzymes and immobilized to enhance cell outgrowth. Stem cell marker expression was detected by reverse transcription-PCR (RT-PCR), and differentiation markers were detected by real-time quantitative RT-PCR and immunocytochemistry. Results showed that dental pulp stem cells actively expressed nanog, oct4, nucleostemin slain-l, jmjdla, jmjd2c, and cyclin DI. When stem cells were induced to differentiate into neurons, nucleostemin, nanog, and cyclin D1 expression significantly decreased, whereas expression of neuronal markers, such as microtubule associated protein-2 and neurofilament-heavy, significantly increased. These results suggested that stem cells exited a pluripotent state and entered a neuronal differentiation pathway. In addition, results demonstrated that human dental pulp serves as a reservoir of stem cells that express defined stem cell markers; these cells were easily isolated and were induced to differentiate towards a desired cell lineage.
基金supported by the Water Pollution Control and Management(No.2009ZX07528)
文摘Metabolizing enzymes play important roles in the detoxification of various pollutants in aquatic organisms, thereby they can also be used to provide early-warning signals of environmental risks. Real-time quantitative reverse-transcription polymerase chain reaction assays were developed to quantify cytochrome P450 1A (CYP1A), superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase (CAT), and glutathione-S-transferase (GST) in crucian carp (Carassius auratus). The methods were then used to detect the respective mRNA expression levels in liver tissue in wild crucian carp from the Hun River, North China. CYP1A mRNA expression was significantly up-regulated in fish from stations $5, $6, and $8 (p 〈 0.05). SOD mRNA expression was significantly down-regulated in downstream areas relative to fish from upstream sites (p 〈 0.05); GPx and CAT mRNA expression levels were also down-regulated at $9 (p 〈 0.05). In contrast, GST mRNA expression showed no obvious change between fish collected from up- or downstream areas of the river. Finally, an integrated biomarker response was used to evaluate the integrated impact of pollutants in the Hun River and allow better comprehension of the real toxicological risk of these investigated sites.
文摘The technique of SYBR Green-based quantitative real-time reverse transcription polymerase chain reaction(real-time RT-PCR)was applied to quantitative detect a 764 bp nucleotide sequence containing total coat protein(cp)gene of Cymbidium mosaic virus(CyMV).The plasmid containing the target sequence was constructed to prepare the standard curve and detect the sensitivity.The standard curve was drawn based on the linear relationship between the logarithm(base 10)of the quantity of target sequence and cycle threshold[C(T)].While the concentration of plasmid DNA falling within the range of 2.6×10^(7)to 2.6×10^(2)copies per tube established a regression equation,y=-0.3583x+10.32,and related coefficient:r^(2)=0.995.The real-time RT-PCR assay for CyMV had a minimum detectable quantity of two copies per tube.The naturally infected samples of Phalaenopsis sp.and the artificially inoculated samples of Arachnis sp.with trace CyMV were quantitatively detected using this method.CyMVin the positive samples of Phalaenopsis sp.and Arachnis sp.was confirmed by DNA sequencing and cp gene homeology blast.The results showed that CyMV extracted from the leaves of orchid in Hangzhou,Zhejiang Province,China,could be derived from Kunming city(KM),Yunnan Province,China.This method characterized by high sensitivity,specificity,and precision is suitable for early diagnosis and quantitative detection of CyMV.