The objectives of this study were to isolate and characterize microsatellites from a heat tolerant variety of snap bean (Phaseolus vulgaris L.) in order to generate polymorphic genetic markers linked to quantitative t...The objectives of this study were to isolate and characterize microsatellites from a heat tolerant variety of snap bean (Phaseolus vulgaris L.) in order to generate polymorphic genetic markers linked to quantitative trait loci for heat tolerance. A genomic library contained 400-800 bp inserts was constructed and screened for the presence of (GA/CT) n and (CA/GT) n repeats. The proportion of positive clones yielded estimated of 3.72×10 4 such dinucleotide repeats per genome, roughly comparable to the abundance reported in other eukaryotic genomes. Twenty_six positive clones were sequenced. In contrast to mammalian genomes, the (GA/CT) n motif was much more abundant than the (CA/GT) n motif in these clones. The (GA/CT) n repeats also showed longer average repeat length (mean n =10.4 versus 6.5), suggesting that they are better candidates for yielding polymorphic genetic markers in the snap bean genome.展开更多
Recognition of DNA damage is a critical step for DNA damage-mediated cellular response. XPC is an important DNA damage recognition protein involved in nucleotide excision repair (NER). We have studied the XPC protein ...Recognition of DNA damage is a critical step for DNA damage-mediated cellular response. XPC is an important DNA damage recognition protein involved in nucleotide excision repair (NER). We have studied the XPC protein in cisplatin DNA damaging treatment-mediated cellular response. Comparison of the microarray data from both normal and XPCdefective human fibroblasts identified 861 XPC-responsive genes in the cisplatin treatment (with minimum fold change≥1.5).The cell cycle and cell proliferation-related genes are the most affected genes by the XPC defect in the treatment. Many other cellular function genes, especially the DNA repair and signal transduction-related genes, were also affected by the XPC defect in the treatment. To validate the microarray data, the transcription levels of some microarray-identified genes were also determined by an RT-PCR based real time PCR assay. The real time PCR results are consistent with the microarray data for most of the tested genes, indicating the reliability of the microarray data. To further validate the microarray data, the cisplatin treatment-mediated caspase-3 activation was also determined. The Western blot hybridization results indicate that the XPC defect greatly attenuates the cisplatin treatment-mediated Caspase-3 activation. We elucidated the role of p53 protein in the XPC protein DNA damage recognition-mediated signaling process. The XPC defect reduces the cisplatin treatment-mediated p53 response. These results suggest that the XPC protein plays an important role in the cisplatin treatment-mediated cellular response. It may also suggest a possible mechanism of cancer cell drug resistance.展开更多
The idea of difference sequence spaces was introduced in (Klzmaz, 1981) and this concept was generalized in (Et and Colak, 1995). In this paper we define some difference sequence spaces by a sequence of Orlicz fun...The idea of difference sequence spaces was introduced in (Klzmaz, 1981) and this concept was generalized in (Et and Colak, 1995). In this paper we define some difference sequence spaces by a sequence of Orlicz functions and establish some inclusion relations.展开更多
The expressed sequence tags(ESTs)of Japanese flounder,Paralichthys olivaeeus,were selected from GenBank to identify simple sequence repeats(SSRs)or microsatellites.A bioinformatic analysis of 11111 ESTs identified...The expressed sequence tags(ESTs)of Japanese flounder,Paralichthys olivaeeus,were selected from GenBank to identify simple sequence repeats(SSRs)or microsatellites.A bioinformatic analysis of 11111 ESTs identified 751 SSR-containing ESTs,including 440 dinucleotide,254 trinucleotide,53 tetranueleotide,95 pentanucleotide and 40 hexanucleotide microsatellites respectively.The CA/TG and GA/TC repeats were the most abundant microsatellites.AT-rich types were predominant among trinucleotide and tetranucleotide microsatellites.PCR primers were designed to amplify 10 identified microsatellites loci.The PCR results from eight pairs of primers showed polymorphisms in wild populations.In 30 wild individuals,the mean observed and expected heterozygosities of these 8 polymorphic SSRs were 0.71 and 0.83 respectively and the average PIC value was 0.8.These microsatellite markers should prove to be a useful addition to the microsatellite markers that are now available for this species.展开更多
Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery ...Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery management and aquaculture development programs for this species. In the present study, we have analyzed the genetic diversity in natural populations of Japanese flounder sampled from the Yellow Sea (Qingdao population, QD) and East China Sea (Zhoushan population, ZS) using 10 polymorphic mierosatellite loci and cytochrome c oxidase subunit I (COI) sequencing data. A total of 68 different alleles were observed over 10 microsatellite loci. The total number of alleles per locus ranged from 2 to 9, and the number of genotypes per locus ranged from 3 to 45. The observed heterozygosity and expected heterozygosity in QD were 0.733 and 0.779, respectively, and in ZS the heterozygosity values were 0.708 and 0.783, respectively. Significant departures from Hardy-Weinberg equilibrium were observed in 7 of the 10 microsatellite loci in each of the two populations. The COI sequencing analysis revealed 25 polymorphic sites and 15 haplotypes in the two populations. The haplotype diversity and nucleotide diversity in the QD population were 0.746±0.072 8 and 0.003 34±0.001 03 respectively, and in ZS population the genetic diversity values were 0.712±0.047 0 and 0.003 18±0.000 49, respectively. The microsatellite data (Fst=0.048 7, P〈0.001) and mitochondrial DNA data (Fst=0.128, P〈0.001) both revealed significant genetic differentiation between the two populations. The information on the genetic variation and differentiation in Japanese flounder obtained in this study could be used to set up suitable guidelines for the management and conservation of this species, as well as for managing artificial selection programs. In future studies, more geographically diverse stocks should be used to obtain a deeper understanding of the population structure of Japanese flounder in the China seas and adjacent regions.展开更多
Dynamic numerical simulation of water conditions is useful for reservoir management. In remote semi-arid areas, however, meteorological and hydrological time-series data needed for computation are not frequently measu...Dynamic numerical simulation of water conditions is useful for reservoir management. In remote semi-arid areas, however, meteorological and hydrological time-series data needed for computation are not frequently measured and must be obtained using other information. This paper presents a case study of data generation for the computation of thermal conditions in the Joumine Reservoir, Tunisia. Data from the Wind Finder web site and daily sunshine duration at the nearest weather stations were utilized to generate cloud cover and solar radiation data based on meteorological correlations obtained in Japan, which is located at the same latitude as Tunisia. A time series of inflow water temperature was estimated from air temperature using a numerical filter expressed as a linear second-order differential equation. A numerical simulation using a vertical 2-D (two-dimensional) turbulent flow model for a stratified water body with generated data successfully reproduced seasonal thermal conditions in the reservoir, which were monitored using a thermistor chain.展开更多
The Wayland algorithm has been improved in order to evaluate the degree of visible determinism for dynamical systems that generate time series. The objective of this study is to show that the Double-Wayland algorithm ...The Wayland algorithm has been improved in order to evaluate the degree of visible determinism for dynamical systems that generate time series. The objective of this study is to show that the Double-Wayland algorithm can distinguish between time series generated by a deterministic process and those generated by a stochastic process. The authors conducted numerical analysis of the van der Pol equation and a stochastic differential equation as a deterministic process and a Ganssian stochastic process, respectively. In case of large S/N ratios, the noise term did not affect the translation error derived from time series data, but affected that from the temporal differences of time series. In case of larger noise amplitudes, the translation error from the differences was calculated to be approximately 1 using the Double-Wayland algorithm, and it did not vary in magnitude. Furthermore, the translation error derived from the differenced sequences was considered stable against noise. This novel algorithm was applied to the detection of anomalous signals in some fields of engineering, such as the analysis of railway systems and bio-signals.展开更多
The order of weighted sum of noise sequence for stochastic system is estimated by using limit theory in probability. Then the divergence rates of state of unstable AR system driven by noise of martingale difference se...The order of weighted sum of noise sequence for stochastic system is estimated by using limit theory in probability. Then the divergence rates of state of unstable AR system driven by noise of martingale difference sequence are established.展开更多
In this paper, author presents the essential conditions of difference information and class ratio dispersion reducing by logarithm and root sequence. They also point out that although new data is in the range suitable...In this paper, author presents the essential conditions of difference information and class ratio dispersion reducing by logarithm and root sequence. They also point out that although new data is in the range suitable of the model, the error after it returns to original state might be great.展开更多
1,3-Propanediol (PDO) is an important bulk industrial material. It can be produced by microbial fermentation. In this study, the microbial flora of mangrove sediment was screened to identify strains with high produc...1,3-Propanediol (PDO) is an important bulk industrial material. It can be produced by microbial fermentation. In this study, the microbial flora of mangrove sediment was screened to identify strains with high production of PDO by fermentation of glycerol. The PDO productivities of the isolated strains were tested, and the strain with highest PDO productivity was characterized using the API20E and 16-s rRNA sequence analysis. The physiological and phylogenetic analysis indicated that the strain was closed related to K. pneumoniae species and was named as K. pneumoniae HSL4. The structure of the dha cluster which was responsible for the biosynthesis of PDO was analyzed. It is observed that K. pneumoniae HSL4 was tolerant to salt and partly tolerant to acetate and lactate, which will favor industrial applications. Fed-batch fermentation experiments revealed K. pneumoniae HSL4 exhibited an excellent ability to produce PDO with high concentration (80.08 g L^-1), productivity (2.22 g L^-1h^-1) and conversion (0.435 g g^-1 or 0.53 mol mol^-1). The metabolic flux profile illuminated that glycerol was consumed rapidly and PDO was accumulated quickly to a high level during the exponential growth phase. This study provided important information for further fermentation and metabolic engineering of PDO production by K. pneumoniae HSL4.展开更多
This paper provides a first indication that this is true for a system comprised of a static structure described by hyperbolic partial differential equations and is subjected to an external random input force. The syst...This paper provides a first indication that this is true for a system comprised of a static structure described by hyperbolic partial differential equations and is subjected to an external random input force. The system deforms the randomness of an input force sequence in proportion to its algorithmic complexity. The authors demonstrate this by numerical analysis of a one-dimensional vibrating elastic solid (the system) on which we apply a maximally-random force sequence (input). The level of complexity of the system is controlled via external parameters. The output response is the field of displacements observed at several positions on the body. The algorithmic complexity and stochasticity of the resulting output displacement sequence is measured and compared against the complexity of the system. The results show that the higher the system complexity, the more random-deficient the output sequence.展开更多
基金Supported by the Tian Yuan Special Funds of the National Natural Science Foundation of China(11626126)the Science and Technology Foundation of Jiangxi Educational Committee(GJJ150080)the Humanities and Social Science Research Project of Colleges and Universities in Jiangxi province(GL1578)
文摘The objectives of this study were to isolate and characterize microsatellites from a heat tolerant variety of snap bean (Phaseolus vulgaris L.) in order to generate polymorphic genetic markers linked to quantitative trait loci for heat tolerance. A genomic library contained 400-800 bp inserts was constructed and screened for the presence of (GA/CT) n and (CA/GT) n repeats. The proportion of positive clones yielded estimated of 3.72×10 4 such dinucleotide repeats per genome, roughly comparable to the abundance reported in other eukaryotic genomes. Twenty_six positive clones were sequenced. In contrast to mammalian genomes, the (GA/CT) n motif was much more abundant than the (CA/GT) n motif in these clones. The (GA/CT) n repeats also showed longer average repeat length (mean n =10.4 versus 6.5), suggesting that they are better candidates for yielding polymorphic genetic markers in the snap bean genome.
文摘Recognition of DNA damage is a critical step for DNA damage-mediated cellular response. XPC is an important DNA damage recognition protein involved in nucleotide excision repair (NER). We have studied the XPC protein in cisplatin DNA damaging treatment-mediated cellular response. Comparison of the microarray data from both normal and XPCdefective human fibroblasts identified 861 XPC-responsive genes in the cisplatin treatment (with minimum fold change≥1.5).The cell cycle and cell proliferation-related genes are the most affected genes by the XPC defect in the treatment. Many other cellular function genes, especially the DNA repair and signal transduction-related genes, were also affected by the XPC defect in the treatment. To validate the microarray data, the transcription levels of some microarray-identified genes were also determined by an RT-PCR based real time PCR assay. The real time PCR results are consistent with the microarray data for most of the tested genes, indicating the reliability of the microarray data. To further validate the microarray data, the cisplatin treatment-mediated caspase-3 activation was also determined. The Western blot hybridization results indicate that the XPC defect greatly attenuates the cisplatin treatment-mediated Caspase-3 activation. We elucidated the role of p53 protein in the XPC protein DNA damage recognition-mediated signaling process. The XPC defect reduces the cisplatin treatment-mediated p53 response. These results suggest that the XPC protein plays an important role in the cisplatin treatment-mediated cellular response. It may also suggest a possible mechanism of cancer cell drug resistance.
文摘The idea of difference sequence spaces was introduced in (Klzmaz, 1981) and this concept was generalized in (Et and Colak, 1995). In this paper we define some difference sequence spaces by a sequence of Orlicz functions and establish some inclusion relations.
基金supported by the National High Technology Research and Development Program of China (Grant No.2006AA10A404)the National Natural Science Foundation of China (Grant No.30671624)
文摘The expressed sequence tags(ESTs)of Japanese flounder,Paralichthys olivaeeus,were selected from GenBank to identify simple sequence repeats(SSRs)or microsatellites.A bioinformatic analysis of 11111 ESTs identified 751 SSR-containing ESTs,including 440 dinucleotide,254 trinucleotide,53 tetranueleotide,95 pentanucleotide and 40 hexanucleotide microsatellites respectively.The CA/TG and GA/TC repeats were the most abundant microsatellites.AT-rich types were predominant among trinucleotide and tetranucleotide microsatellites.PCR primers were designed to amplify 10 identified microsatellites loci.The PCR results from eight pairs of primers showed polymorphisms in wild populations.In 30 wild individuals,the mean observed and expected heterozygosities of these 8 polymorphic SSRs were 0.71 and 0.83 respectively and the average PIC value was 0.8.These microsatellite markers should prove to be a useful addition to the microsatellite markers that are now available for this species.
基金Supported by the Project of Zhejiang Province of China (Nos.2009C12078, 2010F20006, 2010R411054, 2010R50025)
文摘Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery management and aquaculture development programs for this species. In the present study, we have analyzed the genetic diversity in natural populations of Japanese flounder sampled from the Yellow Sea (Qingdao population, QD) and East China Sea (Zhoushan population, ZS) using 10 polymorphic mierosatellite loci and cytochrome c oxidase subunit I (COI) sequencing data. A total of 68 different alleles were observed over 10 microsatellite loci. The total number of alleles per locus ranged from 2 to 9, and the number of genotypes per locus ranged from 3 to 45. The observed heterozygosity and expected heterozygosity in QD were 0.733 and 0.779, respectively, and in ZS the heterozygosity values were 0.708 and 0.783, respectively. Significant departures from Hardy-Weinberg equilibrium were observed in 7 of the 10 microsatellite loci in each of the two populations. The COI sequencing analysis revealed 25 polymorphic sites and 15 haplotypes in the two populations. The haplotype diversity and nucleotide diversity in the QD population were 0.746±0.072 8 and 0.003 34±0.001 03 respectively, and in ZS population the genetic diversity values were 0.712±0.047 0 and 0.003 18±0.000 49, respectively. The microsatellite data (Fst=0.048 7, P〈0.001) and mitochondrial DNA data (Fst=0.128, P〈0.001) both revealed significant genetic differentiation between the two populations. The information on the genetic variation and differentiation in Japanese flounder obtained in this study could be used to set up suitable guidelines for the management and conservation of this species, as well as for managing artificial selection programs. In future studies, more geographically diverse stocks should be used to obtain a deeper understanding of the population structure of Japanese flounder in the China seas and adjacent regions.
文摘Dynamic numerical simulation of water conditions is useful for reservoir management. In remote semi-arid areas, however, meteorological and hydrological time-series data needed for computation are not frequently measured and must be obtained using other information. This paper presents a case study of data generation for the computation of thermal conditions in the Joumine Reservoir, Tunisia. Data from the Wind Finder web site and daily sunshine duration at the nearest weather stations were utilized to generate cloud cover and solar radiation data based on meteorological correlations obtained in Japan, which is located at the same latitude as Tunisia. A time series of inflow water temperature was estimated from air temperature using a numerical filter expressed as a linear second-order differential equation. A numerical simulation using a vertical 2-D (two-dimensional) turbulent flow model for a stratified water body with generated data successfully reproduced seasonal thermal conditions in the reservoir, which were monitored using a thermistor chain.
文摘The Wayland algorithm has been improved in order to evaluate the degree of visible determinism for dynamical systems that generate time series. The objective of this study is to show that the Double-Wayland algorithm can distinguish between time series generated by a deterministic process and those generated by a stochastic process. The authors conducted numerical analysis of the van der Pol equation and a stochastic differential equation as a deterministic process and a Ganssian stochastic process, respectively. In case of large S/N ratios, the noise term did not affect the translation error derived from time series data, but affected that from the temporal differences of time series. In case of larger noise amplitudes, the translation error from the differences was calculated to be approximately 1 using the Double-Wayland algorithm, and it did not vary in magnitude. Furthermore, the translation error derived from the differenced sequences was considered stable against noise. This novel algorithm was applied to the detection of anomalous signals in some fields of engineering, such as the analysis of railway systems and bio-signals.
基金This research is supported by Beijing Natural Science Foundation (1042007, 1052007).
文摘The order of weighted sum of noise sequence for stochastic system is estimated by using limit theory in probability. Then the divergence rates of state of unstable AR system driven by noise of martingale difference sequence are established.
文摘In this paper, author presents the essential conditions of difference information and class ratio dispersion reducing by logarithm and root sequence. They also point out that although new data is in the range suitable of the model, the error after it returns to original state might be great.
基金supported by the Scientific Research Project of the Marine Public Welfare Industry of China (201205020-4)Administration of Ocean and Fisheries of Guangdong Province (GD2012-D01-002)
文摘1,3-Propanediol (PDO) is an important bulk industrial material. It can be produced by microbial fermentation. In this study, the microbial flora of mangrove sediment was screened to identify strains with high production of PDO by fermentation of glycerol. The PDO productivities of the isolated strains were tested, and the strain with highest PDO productivity was characterized using the API20E and 16-s rRNA sequence analysis. The physiological and phylogenetic analysis indicated that the strain was closed related to K. pneumoniae species and was named as K. pneumoniae HSL4. The structure of the dha cluster which was responsible for the biosynthesis of PDO was analyzed. It is observed that K. pneumoniae HSL4 was tolerant to salt and partly tolerant to acetate and lactate, which will favor industrial applications. Fed-batch fermentation experiments revealed K. pneumoniae HSL4 exhibited an excellent ability to produce PDO with high concentration (80.08 g L^-1), productivity (2.22 g L^-1h^-1) and conversion (0.435 g g^-1 or 0.53 mol mol^-1). The metabolic flux profile illuminated that glycerol was consumed rapidly and PDO was accumulated quickly to a high level during the exponential growth phase. This study provided important information for further fermentation and metabolic engineering of PDO production by K. pneumoniae HSL4.
文摘This paper provides a first indication that this is true for a system comprised of a static structure described by hyperbolic partial differential equations and is subjected to an external random input force. The system deforms the randomness of an input force sequence in proportion to its algorithmic complexity. The authors demonstrate this by numerical analysis of a one-dimensional vibrating elastic solid (the system) on which we apply a maximally-random force sequence (input). The level of complexity of the system is controlled via external parameters. The output response is the field of displacements observed at several positions on the body. The algorithmic complexity and stochasticity of the resulting output displacement sequence is measured and compared against the complexity of the system. The results show that the higher the system complexity, the more random-deficient the output sequence.