Paw San Hmwe （PSM） rice has been cultivated in many areas of Myanmar for a long time. Strong aroma, good taste and its elongation during cooking are the key characteristics of PSM rice. Thirty-one PSM accessions wer...Paw San Hmwe （PSM） rice has been cultivated in many areas of Myanmar for a long time. Strong aroma, good taste and its elongation during cooking are the key characteristics of PSM rice. Thirty-one PSM accessions were genotypically characterized, and their physical grain and cooking quality traits were studied. We used specific gene markers associated with aroma, apparent amylose content （AAC） and alkali spreading value to determine the alleles carried by different PSM accessions. The results revealed that six PSM accessions （PSM10, PSM12, PSM13, PSM21, PSM22 and PSM30） had a 3-bp insertion in Os2AP gene. Gel consistency （GC） allele was predominant among the PSM accessions for gelatinization temperature （GT）, however, the phenotype observed was between low and intermediate GT because of the combination of the GC allele with the presence of low GT allele at heterozygous state from the other loci of the SSIla gene. Intermediate to high AAC was observed among the PSM accessions corresponding to the haplotype identified for the single nucleotide polymorphism G/T and the （Cm）n repeat in the Wx gene. The characterization and grouping data of PSM accessions posted benefits to Myanmar seed banks, and our results will help in maintaining the integrity of PSM rice variety.展开更多
The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approa...The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.展开更多
The extensive utilization of the low-energy dipeptide sweetener aspartame in foods leads to various studies on searching for new sweeteners in series. However, the real mechanistic cause of their sweetness power is st...The extensive utilization of the low-energy dipeptide sweetener aspartame in foods leads to various studies on searching for new sweeteners in series. However, the real mechanistic cause of their sweetness power is still not completely known owing to their complex interactions with human sweet receptor, which may be different from that of other sweeteners to some extent. In this contribution, predictive quantitative structure-property relationship(QSPR) models have been developed for diverse aspartame analogues using Materials Studio 5.0 software. The optimal QSPR model(r2 = 0.913, r2 CV = 0.881 and r2 pred = 0.730) constructed by the genetic function approximation method has been validated by the tests of cross validation, randomization, external prediction and other statistical criteria, which shows that their sweetness power is mainly governed by their electrotopological-state indices(SssCH and SsNH), spatial descriptors(Shadow length: LX, ellipsoidal volume and Connolly surface occupied volume) and topological descriptors(Chi(3): cluster and Chi(0)(valence modified)), which partially supports both multipoint attachment theory proposed by Nofre and Tinti et al. and B-X theory proposed by Kier et al.. Present exploited results provide the key structural features for the sweetness power of aspartame analogues, supplement the mechanistic understanding of the sweet perception, and would be also helpful for the design of potent sweetener analogs prior to their synthesis.展开更多
Quantitative structure activity relationship （QSAR） studies were performed on 45 anthranilic acid derivatives for their potent allosteric inhibition activities of HCV NSSB polymerase. Genetic algorithm based genetic...Quantitative structure activity relationship （QSAR） studies were performed on 45 anthranilic acid derivatives for their potent allosteric inhibition activities of HCV NSSB polymerase. Genetic algorithm based genetic function approximation （GFA） method of variable selection was used to generate the model. Highly statistically significant model with r^2 = 0.966 and r^2cv = 0.951 was obtained when the number of descriptors in the equation was set to 5. High r^2pred value of 0.884 indicates the good predictive power of the best model. Spatial descriptors of radius of gyration （RadOfGration）, molecular volume （Vm）, length of molecule in the z dimension （Shadow-Zlength）, thermodynamic descriptors of the octanol/water partition coefficient （LogP） and molecular refractivity index （MR） showed enormous contributions to HCV NS5B polymerase inhibition. The validation of the model was done by leave-one-out （LOO） test, randomization tests and external test set prediction. The model gives insight on indispensable structural requirements for the activity and can be used to design more potent analogs against HCV NSSB polymerase.展开更多
AIM： To study the relationship between quantitative structure and pharmacokinetics （QSPkR） of fluorocluinolone antibacterials.METHODS： The pharmacokinetic （PK） parameters of oral fluoroquinolones were collected ...AIM： To study the relationship between quantitative structure and pharmacokinetics （QSPkR） of fluorocluinolone antibacterials.METHODS： The pharmacokinetic （PK） parameters of oral fluoroquinolones were collected from the literature. These pharmacokinetic data were averaged, 19 compounds were used as the training set, and 3 served as the test set. Genetic function approximation （GFA） module of Cerius2 software was used in QSPkR analysis.RESULTS： A small volume and large polarizability and surface area of substituents at C-7 contribute to a large area under the curve （AUC） for fluoroquinolones. Large polarizability and small volume of substituents at N-1 contribute to a long half life elimination.CONCLUSION： QSPkR models can contribute to some fluoroquinolones antibacterials with excellent pharmacokinetic properties.展开更多
Molecular mechanisms of plant responses to salinity stress and the physiological consequences of altered gene expression are reviewed. Extensive use of comparisons with halophytic plants and glycophytos provide a para...Molecular mechanisms of plant responses to salinity stress and the physiological consequences of altered gene expression are reviewed. Extensive use of comparisons with halophytic plants and glycophytos provide a paradigm for many responses to salinity exhibited by stress sensitive plants. Osmolyte biosynthesis, water flux control, and membrane transport of ions are important for maintenance and re-establishment of homeostasis. Transgenic plant and mutant analyses in Arabidopsis improve the understanding of stress responses and elements of stress signal transduction pathways. The genomic DNA sequences and cell-specific transcript expression data, combined with determinant identification based on molecular genetics, will provide the infrastructure for functional physiological dissection of salt tolerance determinants in plants. Protein interaction analysis, genetic activation and suppression screens will lead inevitably to an understanding of the interrelationships of the multiple signaling systems that control stress-adaptive responses and provide more opportunity to engineer salt tolerance in plants.展开更多
The objective in this experimental article is to gain evidential proof of near-dead cells, (sick-cells in relapse tumor) responding with recovery growth from special 4n, multi-chromatid chromosomes. Note, near-dead &l...The objective in this experimental article is to gain evidential proof of near-dead cells, (sick-cells in relapse tumor) responding with recovery growth from special 4n, multi-chromatid chromosomes. Note, near-dead </span><i><span style="font-family:Verdana;">normal human cells</span></i><span style="font-family:Verdana;"> with such converted chromosome structure gave rise to proliferative, fitness-gained, diploid </span><i><span style="font-family:Verdana;">first cells</span></i><span style="font-family:Verdana;">,</span><i> </i><span style="font-family:Verdana;">which</span><i> </i><span style="font-family:Verdana;">further gave rise to three different cell shape changed, recovery growth patterns. Previously, two cell shape changes had been recovered from same type normal human cells, transiently exposed to amino acid glutamine deficient growth medium with recovery growths also associated with presence of the special 4n cells. The 4n cell-division had been concluded to be a meiotic-like two-step division system to the fitness-gained diploid cells in numerous experiments. The main characteristi</span><span style="font-family:Verdana;">cs of this division system, was firstly whole genomes without polar oriented bent centromeres moving apart followed by much rarer simple fission division to two or three diploid cells, selectable for first cell proliferatio</span><span style="font-family:Verdana;">n. In general these 4n cells showed metaphase type rosette figures moving apart not in the normal spindle associated mitotic shape with centromeres polar-pointing with sloping arms. This sequence of events induced by glutamine-deficiency, was earlier shown to cause DNA breakage in metabolic studies however, the near-death condition was only assumed from normal fibro-blastic cell-sheet shrinkage. This was rectified by an RNA virus (Coxakie-B3), which virology known is a highly cell killing virus (4+ CPE on their scale). This virus replicates only in replicating cells, which led to recovery growths with progressive phenotypic cell-shape changes (spindle, polygonal and roundness cells), each intervened by “total” cell destruction. These three different growth patterns </span><span style="font-family:Verdana;">had morphologies, indistinguishably from today’s cancer diagnostic morphologies. “Mitotic” analyses of beginning growths for the three phenotypes revealed the special rosette figure separations from special 4n and higher ploidy level cells, and also total absence of spindle type mitoses. Tumorigenesis-relevant </span><span style="font-family:Verdana;">was centromere-puffing with premature chromatid separation, and chromatin compaction, a mechanism, that was suggested to protect the genome from damage (text). We suggest that the multi-chromatid polyploid cells with their genome reductive division system, can be a tractable </span><i><span style="font-family:Verdana;">in vitro</span></i><span style="font-family:Verdana;"> model system for therapy information, when repeated from a cell-killing agent, producing virus-free recovery growths. Will it be enacted upon? Not likely with profit-greedy industrial Goliath in the helm of cancer research. But, a not for profit cancer organization, could change this appalling situation.展开更多
Fertilization mode affects soil quality and ecological health.The effects of four fertilization regimens on lignocellulose content,readily degradable carbohydrate decomposition,and potential microbial functions in the...Fertilization mode affects soil quality and ecological health.The effects of four fertilization regimens on lignocellulose content,readily degradable carbohydrate decomposition,and potential microbial functions in the topsoil of a wheat-maize rotation system between 2012 and 2017 were investigated.The fertilization regimens of control(control NFNB),high chemical fertilizer(HCF),high biochar plus low chemical fertilizer(HBLCF),and biochar-based fertilizer(BBF)were compared on soil fundamental properties,microbial structure,and potential function in soil carbohydrate degradation based on metagenome analysis.The diversity of carbohydrate-active enzyme genes in the topsoil microbial consortia in the four trials was primarily distributed within the ten ecologically most dominant phyla.Application of BBF was associated with the lowest decline in total nitrogen and P2O5(2012-2017:6.5%and 28.1%,respectively)and the most effective carbohydrate decomposition(2015-2017:67.0%for cellulose and 59.9%for readily degradable carbohydrate).Carbohydrate transport and metabolism accounted for 6.0%of reads assigned functional classification under the BBF regimen.These findings reveal the ecologically functional diversity of topsoil microorganisms and suggest BBF application as a promising strategy for sustainable agriculture and beneficial to soil health.展开更多
After the consideration of the nonlinear nature changes of monsoon index,and the subjective determination of network structure in traditional artificial neural network prediction modeling,monthly and seasonal monsoon ...After the consideration of the nonlinear nature changes of monsoon index,and the subjective determination of network structure in traditional artificial neural network prediction modeling,monthly and seasonal monsoon intensity index prediction is studied in this paper by using nonlinear genetic neural network ensemble prediction（GNNEP）modeling.It differs from traditional prediction modeling in the following aspects： （1）Input factors of the GNNEP model of monsoon index were selected from a large quantity of preceding period high correlation factors,such as monthly sea temperature fields,monthly 500-hPa air temperature fields,monthly 200-hPa geopotential height fields,etc.,and they were also highly information-condensed and system dimensionality-reduced by using the empirical orthogonal function（EOF）method,which effectively condensed the useful information of predictors and therefore controlled the size of network structure of the GNNEP model.（2）In the input design of the GNNEP model,a mean generating function（MGF）series of predictand（monsoon index）was added as an input factor;the contrast analysis of results of predic- tion experiments by a physical variable predictor-predictand MGF GNNEP model and a physical variable predictor GNNEP model shows that the incorporation of the periodical variation of predictand（monsoon index）is very effective in improving the prediction of monsoon index.（3）Different from the traditional neural network modeling,the GNNEP modeling is able to objectively determine the network structure of the GNNNEP model,and the model constructed has a better generalization capability.In the case of identical predictors,prediction modeling samples,and independent prediction samples,the prediction accuracy of our GNNEP model combined with the system dimensionality reduction technique of predictors is clearly higher than that of the traditional stepwise regression model using the traditional treatment technique of predictors,suggesting that the GNNEP model opens up a vast range of possibilities for operational weather prediction.展开更多
基金supported by the National Center for Genetic Engineering and Biotechnology,Thailand (Grant No.P1020028)Generation Challenge Program,Mexico (Grant No.P0900835)
文摘Paw San Hmwe （PSM） rice has been cultivated in many areas of Myanmar for a long time. Strong aroma, good taste and its elongation during cooking are the key characteristics of PSM rice. Thirty-one PSM accessions were genotypically characterized, and their physical grain and cooking quality traits were studied. We used specific gene markers associated with aroma, apparent amylose content （AAC） and alkali spreading value to determine the alleles carried by different PSM accessions. The results revealed that six PSM accessions （PSM10, PSM12, PSM13, PSM21, PSM22 and PSM30） had a 3-bp insertion in Os2AP gene. Gel consistency （GC） allele was predominant among the PSM accessions for gelatinization temperature （GT）, however, the phenotype observed was between low and intermediate GT because of the combination of the GC allele with the presence of low GT allele at heterozygous state from the other loci of the SSIla gene. Intermediate to high AAC was observed among the PSM accessions corresponding to the haplotype identified for the single nucleotide polymorphism G/T and the （Cm）n repeat in the Wx gene. The characterization and grouping data of PSM accessions posted benefits to Myanmar seed banks, and our results will help in maintaining the integrity of PSM rice variety.
文摘The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.
基金Supported by the National Natural Science Foundation of China(No.21673207)Special Fundamental Research Fund for the Central Public Scientific Research Institutes(No.562018Y-5983)Zhejiang Provincial Collaborative Innovation Center of Food Safety and Nutrition(No.2017SICR115,2017SICR101)
文摘The extensive utilization of the low-energy dipeptide sweetener aspartame in foods leads to various studies on searching for new sweeteners in series. However, the real mechanistic cause of their sweetness power is still not completely known owing to their complex interactions with human sweet receptor, which may be different from that of other sweeteners to some extent. In this contribution, predictive quantitative structure-property relationship(QSPR) models have been developed for diverse aspartame analogues using Materials Studio 5.0 software. The optimal QSPR model(r2 = 0.913, r2 CV = 0.881 and r2 pred = 0.730) constructed by the genetic function approximation method has been validated by the tests of cross validation, randomization, external prediction and other statistical criteria, which shows that their sweetness power is mainly governed by their electrotopological-state indices(SssCH and SsNH), spatial descriptors(Shadow length: LX, ellipsoidal volume and Connolly surface occupied volume) and topological descriptors(Chi(3): cluster and Chi(0)(valence modified)), which partially supports both multipoint attachment theory proposed by Nofre and Tinti et al. and B-X theory proposed by Kier et al.. Present exploited results provide the key structural features for the sweetness power of aspartame analogues, supplement the mechanistic understanding of the sweet perception, and would be also helpful for the design of potent sweetener analogs prior to their synthesis.
基金supported by the National Natural Science Foundation of China (No. 30500339)Natural Science Foundation of Zhejiang Province (NO.Y407308)the Sprout Talented Project Program of Zhejiang Province (No. 2008R40G2020019)
文摘Quantitative structure activity relationship （QSAR） studies were performed on 45 anthranilic acid derivatives for their potent allosteric inhibition activities of HCV NSSB polymerase. Genetic algorithm based genetic function approximation （GFA） method of variable selection was used to generate the model. Highly statistically significant model with r^2 = 0.966 and r^2cv = 0.951 was obtained when the number of descriptors in the equation was set to 5. High r^2pred value of 0.884 indicates the good predictive power of the best model. Spatial descriptors of radius of gyration （RadOfGration）, molecular volume （Vm）, length of molecule in the z dimension （Shadow-Zlength）, thermodynamic descriptors of the octanol/water partition coefficient （LogP） and molecular refractivity index （MR） showed enormous contributions to HCV NS5B polymerase inhibition. The validation of the model was done by leave-one-out （LOO） test, randomization tests and external test set prediction. The model gives insight on indispensable structural requirements for the activity and can be used to design more potent analogs against HCV NSSB polymerase.
基金the National Basic Research Program of China,No. 2004BC518902
文摘AIM： To study the relationship between quantitative structure and pharmacokinetics （QSPkR） of fluorocluinolone antibacterials.METHODS： The pharmacokinetic （PK） parameters of oral fluoroquinolones were collected from the literature. These pharmacokinetic data were averaged, 19 compounds were used as the training set, and 3 served as the test set. Genetic function approximation （GFA） module of Cerius2 software was used in QSPkR analysis.RESULTS： A small volume and large polarizability and surface area of substituents at C-7 contribute to a large area under the curve （AUC） for fluoroquinolones. Large polarizability and small volume of substituents at N-1 contribute to a long half life elimination.CONCLUSION： QSPkR models can contribute to some fluoroquinolones antibacterials with excellent pharmacokinetic properties.
文摘Molecular mechanisms of plant responses to salinity stress and the physiological consequences of altered gene expression are reviewed. Extensive use of comparisons with halophytic plants and glycophytos provide a paradigm for many responses to salinity exhibited by stress sensitive plants. Osmolyte biosynthesis, water flux control, and membrane transport of ions are important for maintenance and re-establishment of homeostasis. Transgenic plant and mutant analyses in Arabidopsis improve the understanding of stress responses and elements of stress signal transduction pathways. The genomic DNA sequences and cell-specific transcript expression data, combined with determinant identification based on molecular genetics, will provide the infrastructure for functional physiological dissection of salt tolerance determinants in plants. Protein interaction analysis, genetic activation and suppression screens will lead inevitably to an understanding of the interrelationships of the multiple signaling systems that control stress-adaptive responses and provide more opportunity to engineer salt tolerance in plants.
文摘The objective in this experimental article is to gain evidential proof of near-dead cells, (sick-cells in relapse tumor) responding with recovery growth from special 4n, multi-chromatid chromosomes. Note, near-dead </span><i><span style="font-family:Verdana;">normal human cells</span></i><span style="font-family:Verdana;"> with such converted chromosome structure gave rise to proliferative, fitness-gained, diploid </span><i><span style="font-family:Verdana;">first cells</span></i><span style="font-family:Verdana;">,</span><i> </i><span style="font-family:Verdana;">which</span><i> </i><span style="font-family:Verdana;">further gave rise to three different cell shape changed, recovery growth patterns. Previously, two cell shape changes had been recovered from same type normal human cells, transiently exposed to amino acid glutamine deficient growth medium with recovery growths also associated with presence of the special 4n cells. The 4n cell-division had been concluded to be a meiotic-like two-step division system to the fitness-gained diploid cells in numerous experiments. The main characteristi</span><span style="font-family:Verdana;">cs of this division system, was firstly whole genomes without polar oriented bent centromeres moving apart followed by much rarer simple fission division to two or three diploid cells, selectable for first cell proliferatio</span><span style="font-family:Verdana;">n. In general these 4n cells showed metaphase type rosette figures moving apart not in the normal spindle associated mitotic shape with centromeres polar-pointing with sloping arms. This sequence of events induced by glutamine-deficiency, was earlier shown to cause DNA breakage in metabolic studies however, the near-death condition was only assumed from normal fibro-blastic cell-sheet shrinkage. This was rectified by an RNA virus (Coxakie-B3), which virology known is a highly cell killing virus (4+ CPE on their scale). This virus replicates only in replicating cells, which led to recovery growths with progressive phenotypic cell-shape changes (spindle, polygonal and roundness cells), each intervened by “total” cell destruction. These three different growth patterns </span><span style="font-family:Verdana;">had morphologies, indistinguishably from today’s cancer diagnostic morphologies. “Mitotic” analyses of beginning growths for the three phenotypes revealed the special rosette figure separations from special 4n and higher ploidy level cells, and also total absence of spindle type mitoses. Tumorigenesis-relevant </span><span style="font-family:Verdana;">was centromere-puffing with premature chromatid separation, and chromatin compaction, a mechanism, that was suggested to protect the genome from damage (text). We suggest that the multi-chromatid polyploid cells with their genome reductive division system, can be a tractable </span><i><span style="font-family:Verdana;">in vitro</span></i><span style="font-family:Verdana;"> model system for therapy information, when repeated from a cell-killing agent, producing virus-free recovery growths. Will it be enacted upon? Not likely with profit-greedy industrial Goliath in the helm of cancer research. But, a not for profit cancer organization, could change this appalling situation.
基金This work was supported by the Profession Scientific Research Special Item of Agricultural Public Welfare of China(Grant No.201503135-2).
文摘Fertilization mode affects soil quality and ecological health.The effects of four fertilization regimens on lignocellulose content,readily degradable carbohydrate decomposition,and potential microbial functions in the topsoil of a wheat-maize rotation system between 2012 and 2017 were investigated.The fertilization regimens of control(control NFNB),high chemical fertilizer(HCF),high biochar plus low chemical fertilizer(HBLCF),and biochar-based fertilizer(BBF)were compared on soil fundamental properties,microbial structure,and potential function in soil carbohydrate degradation based on metagenome analysis.The diversity of carbohydrate-active enzyme genes in the topsoil microbial consortia in the four trials was primarily distributed within the ten ecologically most dominant phyla.Application of BBF was associated with the lowest decline in total nitrogen and P2O5(2012-2017:6.5%and 28.1%,respectively)and the most effective carbohydrate decomposition(2015-2017:67.0%for cellulose and 59.9%for readily degradable carbohydrate).Carbohydrate transport and metabolism accounted for 6.0%of reads assigned functional classification under the BBF regimen.These findings reveal the ecologically functional diversity of topsoil microorganisms and suggest BBF application as a promising strategy for sustainable agriculture and beneficial to soil health.
基金the New Technology Extension Project of China Meteorological Administration under Grant No.GMATG2008M49the National Natural Science Foundation of China under Grant No.40675023
文摘After the consideration of the nonlinear nature changes of monsoon index,and the subjective determination of network structure in traditional artificial neural network prediction modeling,monthly and seasonal monsoon intensity index prediction is studied in this paper by using nonlinear genetic neural network ensemble prediction（GNNEP）modeling.It differs from traditional prediction modeling in the following aspects： （1）Input factors of the GNNEP model of monsoon index were selected from a large quantity of preceding period high correlation factors,such as monthly sea temperature fields,monthly 500-hPa air temperature fields,monthly 200-hPa geopotential height fields,etc.,and they were also highly information-condensed and system dimensionality-reduced by using the empirical orthogonal function（EOF）method,which effectively condensed the useful information of predictors and therefore controlled the size of network structure of the GNNEP model.（2）In the input design of the GNNEP model,a mean generating function（MGF）series of predictand（monsoon index）was added as an input factor;the contrast analysis of results of predic- tion experiments by a physical variable predictor-predictand MGF GNNEP model and a physical variable predictor GNNEP model shows that the incorporation of the periodical variation of predictand（monsoon index）is very effective in improving the prediction of monsoon index.（3）Different from the traditional neural network modeling,the GNNEP modeling is able to objectively determine the network structure of the GNNNEP model,and the model constructed has a better generalization capability.In the case of identical predictors,prediction modeling samples,and independent prediction samples,the prediction accuracy of our GNNEP model combined with the system dimensionality reduction technique of predictors is clearly higher than that of the traditional stepwise regression model using the traditional treatment technique of predictors,suggesting that the GNNEP model opens up a vast range of possibilities for operational weather prediction.
