This study investigates how financial literacy and behavioral traits affect the adoption of electronic payment(ePayment)services in Japan.We construct a financial literacy index using a representative sample of 25,000...This study investigates how financial literacy and behavioral traits affect the adoption of electronic payment(ePayment)services in Japan.We construct a financial literacy index using a representative sample of 25,000 individuals from the Bank of Japan’s 2019 Financial Literacy Survey.We then analyze the relationship between this index and the extensive and intensive usage of two types of payment services:electronic money(e-money)and mobile payment apps.Using an instrumental variable approach,we find that higher financial literacy is positively associated with a higher likelihood of adopting ePayment services.The empirical results suggest that individuals with higher financial literacy use payment services more frequently.We also find that risk-averse people are less likely to adopt and use ePayment services,whereas people with herd behavior tend to adopt and use ePayment services more.Our empirical results also suggest that the effects of financial literacy on the adoption and use of ePayment differ among people with different behavioral traits.展开更多
Manure management is an essential component of dairy production. Nutrient-laden, field-applied dairy manure often serves as a fertilizer source, but can also pose environmental threats if not properly managed. The Haa...Manure management is an essential component of dairy production. Nutrient-laden, field-applied dairy manure often serves as a fertilizer source, but can also pose environmental threats if not properly managed. The Haak dairy farm, located in Decatur, Arkansas, was granted a permit by the Arkansas Department of Environmental Quality (ADEQ) to employ a unique method in treating and storing cattle manure generated during the milking process. This method includes minimizing water use in wash water, dry scraping solids to combine with sawdust for composting and pumping effluent underground into a sloped concrete basin that serves as secondary solid separator before transporting the manure effluent into an interception trench and an adjacent grassed field to facilitate manure nutrient uptake and retention. The Arkansas Discovery Farm program (ADF) is conducting research to evaluate the environmental performance of the dairy’s milk center wash water treatment system (MCWW) by statistical analysis, characterization of phosphorus (P) migration in soil downslope from the inception trench, temperature measurements, and nutrient analysis of a stored dry stack manure/sawdust mixture. Goals included determining possible composting effectiveness along with comparisons to untreated dairy manure and quantifying the use of on-farm water. Results from this research demonstrated that: 1) The MCWW was effective at retaining manure-derived nutrients and reducing field nutrient migration as the MCWW interception trench had significantly higher total nitrogen (TN) (804.2 to 4.1), total phosphorus (TP) (135.6 to 1.5), and water extractable phosphorus (WEP) (55.0 to 1.0) concentrations in milligrams per liter (mg⋅L<sup>-1</sup>) than the downhill freshwater pond respectively;2) temperature readings of the manure dry stack indicated heightened levels of microbial and thermal activity, but did not reach a standard composting temperature of 54°C;3) manure dry stack nutrient content was typically higher than untreated dairy manure when measured on a “dry basis” in ppm, but was lower on an “as is basis” in ppm and kg/metric ton;and 4) water meter readings showed that the greatest use of on-farm water was for farm-wide cattle drinking (18.77), followed by water used in the milking center (3.45) and then followed by human usage (0.02) measured in cubic meters per day (m<sup>3</sup>⋅d<sup>-1</sup>). These results demonstrate that practical innovations in agricultural engineering and environmental science, such as the Haak dairy’s manure treatment system, can effectively reduce environmental hazards that accompany the management of manure at this dairy operation.展开更多
This work;It was made to determine the positive and negative usage information, attitudes and behaviors of social networking networks for users. Today, it is well known how the wide social effects of social networking...This work;It was made to determine the positive and negative usage information, attitudes and behaviors of social networking networks for users. Today, it is well known how the wide social effects of social networking sites are widespread and effective. As far as it can be followed from written and visual media, it causes significant damages for attitudes and behaviors for individuals. Looking at the results of the study, it seems impossible to limit the time and necessity of these networks for people, but it is understood that people force their limits and capacity. It was determined that the general acceptance and rejection areas are mixed and the dominant distinctive effects were weakened. Unable to prevent social dissolution and deterioration was realized by these social networks of networks. However, we cannot only talk about negative effects because their positive effects should be mentioned. Data were obtained in this direction. For example, some segments encourage the users of these sites to have more freedom, to develop democracy and human rights awareness. However, the real problem is when and where to stand. This study;Social networking networks use information, attitudes and behaviors;It was carried out for the purpose of evaluating the use of nicknames and networks for the use of networks. The data of the study were obtained by the application of a questionnaire and the data obtained were analyzed with appropriate statistical analysis methods. In the first part of the study, field study/operational concept scanning is performed and theoretical information is included. In the second part, the purpose of the study, the problem status, the importance of the study, limitations, assumptions, problem question, research method, research universe and sample are specified and informed. In the third section, the data obtained using appropriate statistical methods are analyzed. In the last section, some important suggestions and comments are made in the light of the data obtained.展开更多
In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms （i.e., Pyrobaculum aerophilum str. IM2 and Sulfol...In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms （i.e., Pyrobaculum aerophilum str. IM2 and Sulfolobus acidocaldarius DSM 639）. The results indicated that the synonymous codon usage in A. pernix K1 was less biased, which was highly correlated with the GC3s value. The codon usage patterns were phylogenetically conserved among these Crenarchaeota microorganisms. Comparatively, it is the species function rather than the gene function that determines their gene codon usage patterns. A. pernix K1, P. aerophilum str. IM2, and S. acidocaldarius DSM 639 live in differently extreme conditions. It is presumed that the hving environment played an important role in determining the codon usage pattern of these microorganisms. Besides, there was no strain-specific codon usage among these microorganisms. The extent of codon bias in A. pernix K1 and S. acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. aerophilum str. IM2 genomes.展开更多
Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different specie...Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.展开更多
Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstl...Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.展开更多
A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms （Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160...A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms （Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160）. Results revealed that synonymous codon usage in Methanosarcina mazei str. Goel was less biased, which was highly correlated with the GC3S value. And the codon usage patterns were phylogenetically conserved among those Euryarchaeota microorganisms. By employing a hierarchical clustering analysis, it can be seen that it is more the species than the gene function that determines their gene codon usage pattems. Considering that those microorganisms live in different environments where the pH conditions vary quite a lot, it can be presumed that their living environments, especially the pH conditions, play an important role in determining those microorganisms＇ codon usage pattems.展开更多
The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.T...The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.The results indicate that most minor codons for these coronaviruses are preferentially used in the initial and terminal region.The minor codons preferentially used in the initial region are thought to have a negative effect on gene expression,which can be explained by the minor codon modulator hypothesis.It also indicates that the minor codons preferentially used in the terminal region may regulate the level of gene expression.The proposed results strongly imply that the minor codon modulator hypothesis can be applied to both some bacteria and some viruses.展开更多
Ambiguity is a unique linguistic feature and is caused by many factors. This paper first introduces the definitions of ambiguity and then mainly illustrates ambiguity in our daily language usage in both English and Ch...Ambiguity is a unique linguistic feature and is caused by many factors. This paper first introduces the definitions of ambiguity and then mainly illustrates ambiguity in our daily language usage in both English and Chinese from phonetic level and syntactic level. People can learn the relationships among those levels and grasp the rule of learning language. Thus, people can realize the complexity and importance of using language and know that it is not easy to express ideas accurately.展开更多
Based on lawn function theory and urban planning perspectives, functions of urban lawns were analyzed, status and prospect of the multiple usages of lawn were revealed. Urban lawn was concluded as an important part of...Based on lawn function theory and urban planning perspectives, functions of urban lawns were analyzed, status and prospect of the multiple usages of lawn were revealed. Urban lawn was concluded as an important part of modern urban greening, moveover, it has been integrated in people's lives gradually by playing a significant role in people's work, studying, leisure, urban disaster prevention and mitigation. At the same time, problems rise from the multiple usages of lawn were discussed and improvement suggestions were put forward.展开更多
The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis （a commonly used multivariate statistical approach） and method of effective number of codons （ENc）-plo...The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis （a commonly used multivariate statistical approach） and method of effective number of codons （ENc）-plot were conducted to analyze synonymous codon usage. The results of correspondence analysis showed that the distribution of genes on the major axis was significantly correlated with the frequency of use of G＋C in synonymously variable third position of sense codon （GC3S）, （r=0.349）, and the positions of genes on the axis 2 and axis 3 were significantly correlated with CAI （r=-0.348, p〈0.01 and r=0.602, p〈0.01）. The ENc for most genes was similar to that for the expected ENc based on the GC3s, but several genes with low ENc values were lying below the expected curve. All of these data indicated that codon usage was dominated by a mutational bias in chloroplast gcnome ofP. alba. The selection in nature for translational efficiency only played a minor role in shaping codon usage in the chloroplast genome ofP alba.展开更多
Codon usage in chloroplast genome of six seed plants （Arabidopsis thaliana, Populus alba, Zea mays, Triticum aestivum, Pinus koraiensis and Cycas taitungensis） was analyzed to find general patterns of codon usage in...Codon usage in chloroplast genome of six seed plants （Arabidopsis thaliana, Populus alba, Zea mays, Triticum aestivum, Pinus koraiensis and Cycas taitungensis） was analyzed to find general patterns of codon usage in chloroplast genomes of seed plants. The results show that chloroplast genomes of the six seed plants had similar codon usage patterns, with a strong bias towards a high representation of NNA and NNT codons. In chloroplast genomes of the six seed plants, the effective number of codons （ENC） for most genes was similar to that of the expected ENC based on the GC content at the third codon position, but several genes with low ENC values were laying below the expected curve. All of these data indicate that codon usage was dominated by a mutational bias in chloroplast genomes of seed plants and that selection appeared to be limited to a subset of genes and to only subtly affect codon usage. Meantime, four, six, eight, nine, ten and 12 codons were defined as the optimal codons in chloroplast genomes of the six seed plants.展开更多
Codon usage bias(CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast(cp) gene...Codon usage bias(CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast(cp) genes among three tea species, i.e., Camellia sinensis var. assamica(Assam tea), Camellia sinensis var. sinensis(Chinese tea) and Camellia pubicosta(wild tea species) as no work on CUB was reported earlier. To understand the patterns of codon usage among the cp genes of three tea groups, we used bioinformatic tools to investigate the protein coding sequences of cp genes. In our present study, the mean nucleobase T was the highest whereas C was the lowest in all the three tea groups. The overall AT content was more than GC content, i.e., genes were AT rich. The scaled chi-square(SCS) value indicated that the CUB of cp genes was low. The codon CGT(Arg) was over-represented in C. sinensis var. sinensis whereas GGA(Pro) was over-represented in C. pubicosta species. Heatmap study revealed that most of the GC ending codons showed positive correlations between codon usage and GC3 while AT ending codons exhibited negative correlations. From neutrality plot analysis, it was evident that natural selection had played a major role, while mutation pressure exerted a minor effect in the CUB of cp genes in three tea groups. Highly significant(P<0.01) positive correlation was found between SCS and synonymous codon usage order(SCUO) of cp genes which suggested that high expression of cp genes was associated with high degree of CUB.展开更多
Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent oppo...Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by Codon W and SPSS（Statistical Product and Service Solutions） programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple.展开更多
Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes...Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula. In present study, 39 531 available coding sequences （CDSs） from M. truncatula were examined for codon usage bias （CUB）. Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.展开更多
Future or smart community, which mainly refers to the development of community information and communication technology(ICT) platforms or devices, has received considerable attention from urban governments and scholar...Future or smart community, which mainly refers to the development of community information and communication technology(ICT) platforms or devices, has received considerable attention from urban governments and scholars. However, only a few studies have been conducted to test the actual effects of using these community ICT platforms or devices on the community satisfaction of residents. Therefore, the present study conducts a survey in 40 communities in Nanjing, China and uses a mixed linear regression model to determine the relationship between community ICT usage and community satisfaction. Results indicate that residents with high-level community ICT usage are more satisfied with their community than those with low-level community ICT usage. Moreover, evident differences are observed regarding the influence of new commodity, old commodity and affordable housing communities in Nanjing. These findings are meaningful for the construction and development of future communities.展开更多
In order to study the spatiotemporal characteristics of the dockless bike sharing system(BSS)around urban rail transit stations,new normalized calculation methods are proposed to explore the temporal and spatial usage...In order to study the spatiotemporal characteristics of the dockless bike sharing system(BSS)around urban rail transit stations,new normalized calculation methods are proposed to explore the temporal and spatial usage patterns of the dockless BSS around rail transit stations by using 5-weekday dockless bike sharing trip data in Nanjing,China.First,the rail transit station area(RTSA)is defined by extracting shared bike trips with trip ends falling into the area.Then,the temporal and spatial decomposition methods are developed and two criterions are calculated,namely,normalized dynamic variation of bikes(NDVB)and normalized spatial distribution of trips(NSDT).Furthermore,the temporal and spatial usage patterns are clustered and the corresponding geographical distributions of shared bikes are determined.The results show that four temporal usage patterns and two spatial patterns of dockless BSS are finally identified.Area type(urban center and suburb)has a great influence on temporal usage patterns.Spatial usage patterns are irregular and affected by limited directions,adjacent rail transit stations and street networks.The findings can help form a better understanding of dockless shared bike users behavior around rail transit stations,which will contribute to improving the service and efficiency of both rail transit and BSS.展开更多
基金National Foundation for Science and Technology Development(No.502.01-2020.308).
文摘This study investigates how financial literacy and behavioral traits affect the adoption of electronic payment(ePayment)services in Japan.We construct a financial literacy index using a representative sample of 25,000 individuals from the Bank of Japan’s 2019 Financial Literacy Survey.We then analyze the relationship between this index and the extensive and intensive usage of two types of payment services:electronic money(e-money)and mobile payment apps.Using an instrumental variable approach,we find that higher financial literacy is positively associated with a higher likelihood of adopting ePayment services.The empirical results suggest that individuals with higher financial literacy use payment services more frequently.We also find that risk-averse people are less likely to adopt and use ePayment services,whereas people with herd behavior tend to adopt and use ePayment services more.Our empirical results also suggest that the effects of financial literacy on the adoption and use of ePayment differ among people with different behavioral traits.
文摘Manure management is an essential component of dairy production. Nutrient-laden, field-applied dairy manure often serves as a fertilizer source, but can also pose environmental threats if not properly managed. The Haak dairy farm, located in Decatur, Arkansas, was granted a permit by the Arkansas Department of Environmental Quality (ADEQ) to employ a unique method in treating and storing cattle manure generated during the milking process. This method includes minimizing water use in wash water, dry scraping solids to combine with sawdust for composting and pumping effluent underground into a sloped concrete basin that serves as secondary solid separator before transporting the manure effluent into an interception trench and an adjacent grassed field to facilitate manure nutrient uptake and retention. The Arkansas Discovery Farm program (ADF) is conducting research to evaluate the environmental performance of the dairy’s milk center wash water treatment system (MCWW) by statistical analysis, characterization of phosphorus (P) migration in soil downslope from the inception trench, temperature measurements, and nutrient analysis of a stored dry stack manure/sawdust mixture. Goals included determining possible composting effectiveness along with comparisons to untreated dairy manure and quantifying the use of on-farm water. Results from this research demonstrated that: 1) The MCWW was effective at retaining manure-derived nutrients and reducing field nutrient migration as the MCWW interception trench had significantly higher total nitrogen (TN) (804.2 to 4.1), total phosphorus (TP) (135.6 to 1.5), and water extractable phosphorus (WEP) (55.0 to 1.0) concentrations in milligrams per liter (mg⋅L<sup>-1</sup>) than the downhill freshwater pond respectively;2) temperature readings of the manure dry stack indicated heightened levels of microbial and thermal activity, but did not reach a standard composting temperature of 54°C;3) manure dry stack nutrient content was typically higher than untreated dairy manure when measured on a “dry basis” in ppm, but was lower on an “as is basis” in ppm and kg/metric ton;and 4) water meter readings showed that the greatest use of on-farm water was for farm-wide cattle drinking (18.77), followed by water used in the milking center (3.45) and then followed by human usage (0.02) measured in cubic meters per day (m<sup>3</sup>⋅d<sup>-1</sup>). These results demonstrate that practical innovations in agricultural engineering and environmental science, such as the Haak dairy’s manure treatment system, can effectively reduce environmental hazards that accompany the management of manure at this dairy operation.
文摘This work;It was made to determine the positive and negative usage information, attitudes and behaviors of social networking networks for users. Today, it is well known how the wide social effects of social networking sites are widespread and effective. As far as it can be followed from written and visual media, it causes significant damages for attitudes and behaviors for individuals. Looking at the results of the study, it seems impossible to limit the time and necessity of these networks for people, but it is understood that people force their limits and capacity. It was determined that the general acceptance and rejection areas are mixed and the dominant distinctive effects were weakened. Unable to prevent social dissolution and deterioration was realized by these social networks of networks. However, we cannot only talk about negative effects because their positive effects should be mentioned. Data were obtained in this direction. For example, some segments encourage the users of these sites to have more freedom, to develop democracy and human rights awareness. However, the real problem is when and where to stand. This study;Social networking networks use information, attitudes and behaviors;It was carried out for the purpose of evaluating the use of nicknames and networks for the use of networks. The data of the study were obtained by the application of a questionnaire and the data obtained were analyzed with appropriate statistical analysis methods. In the first part of the study, field study/operational concept scanning is performed and theoretical information is included. In the second part, the purpose of the study, the problem status, the importance of the study, limitations, assumptions, problem question, research method, research universe and sample are specified and informed. In the third section, the data obtained using appropriate statistical methods are analyzed. In the last section, some important suggestions and comments are made in the light of the data obtained.
基金The work is supported by National Natural Science Foundation of China (No. 60121101).
文摘In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms （i.e., Pyrobaculum aerophilum str. IM2 and Sulfolobus acidocaldarius DSM 639）. The results indicated that the synonymous codon usage in A. pernix K1 was less biased, which was highly correlated with the GC3s value. The codon usage patterns were phylogenetically conserved among these Crenarchaeota microorganisms. Comparatively, it is the species function rather than the gene function that determines their gene codon usage patterns. A. pernix K1, P. aerophilum str. IM2, and S. acidocaldarius DSM 639 live in differently extreme conditions. It is presumed that the hving environment played an important role in determining the codon usage pattern of these microorganisms. Besides, there was no strain-specific codon usage among these microorganisms. The extent of codon bias in A. pernix K1 and S. acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. aerophilum str. IM2 genomes.
基金This work was supported by the National Major Basic Research and Development Program(No.TG1999016004)Jiangsu Provincial Natural Science Foundation(No.BK2003213).
文摘Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.
文摘Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.
文摘A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms （Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160）. Results revealed that synonymous codon usage in Methanosarcina mazei str. Goel was less biased, which was highly correlated with the GC3S value. And the codon usage patterns were phylogenetically conserved among those Euryarchaeota microorganisms. By employing a hierarchical clustering analysis, it can be seen that it is more the species than the gene function that determines their gene codon usage pattems. Considering that those microorganisms live in different environments where the pH conditions vary quite a lot, it can be presumed that their living environments, especially the pH conditions, play an important role in determining those microorganisms＇ codon usage pattems.
文摘The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.The results indicate that most minor codons for these coronaviruses are preferentially used in the initial and terminal region.The minor codons preferentially used in the initial region are thought to have a negative effect on gene expression,which can be explained by the minor codon modulator hypothesis.It also indicates that the minor codons preferentially used in the terminal region may regulate the level of gene expression.The proposed results strongly imply that the minor codon modulator hypothesis can be applied to both some bacteria and some viruses.
文摘Ambiguity is a unique linguistic feature and is caused by many factors. This paper first introduces the definitions of ambiguity and then mainly illustrates ambiguity in our daily language usage in both English and Chinese from phonetic level and syntactic level. People can learn the relationships among those levels and grasp the rule of learning language. Thus, people can realize the complexity and importance of using language and know that it is not easy to express ideas accurately.
文摘Based on lawn function theory and urban planning perspectives, functions of urban lawns were analyzed, status and prospect of the multiple usages of lawn were revealed. Urban lawn was concluded as an important part of modern urban greening, moveover, it has been integrated in people's lives gradually by playing a significant role in people's work, studying, leisure, urban disaster prevention and mitigation. At the same time, problems rise from the multiple usages of lawn were discussed and improvement suggestions were put forward.
基金supported by the National High Tech Development Project of Chinathe 863 Program (Grant Nos.2007AA02Z329)the National Natural Science Foundation of China (Grant Nos.20060213024).
文摘The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis （a commonly used multivariate statistical approach） and method of effective number of codons （ENc）-plot were conducted to analyze synonymous codon usage. The results of correspondence analysis showed that the distribution of genes on the major axis was significantly correlated with the frequency of use of G＋C in synonymously variable third position of sense codon （GC3S）, （r=0.349）, and the positions of genes on the axis 2 and axis 3 were significantly correlated with CAI （r=-0.348, p〈0.01 and r=0.602, p〈0.01）. The ENc for most genes was similar to that for the expected ENc based on the GC3s, but several genes with low ENc values were lying below the expected curve. All of these data indicated that codon usage was dominated by a mutational bias in chloroplast gcnome ofP. alba. The selection in nature for translational efficiency only played a minor role in shaping codon usage in the chloroplast genome ofP alba.
基金supported in part by the Hi-Tech Re-search and Development Program of China ("863" Program) (No. 2007AA02Z329)the National Natural Science Foundation of China (Grant No. 20060213024)
文摘Codon usage in chloroplast genome of six seed plants （Arabidopsis thaliana, Populus alba, Zea mays, Triticum aestivum, Pinus koraiensis and Cycas taitungensis） was analyzed to find general patterns of codon usage in chloroplast genomes of seed plants. The results show that chloroplast genomes of the six seed plants had similar codon usage patterns, with a strong bias towards a high representation of NNA and NNT codons. In chloroplast genomes of the six seed plants, the effective number of codons （ENC） for most genes was similar to that of the expected ENC based on the GC content at the third codon position, but several genes with low ENC values were laying below the expected curve. All of these data indicate that codon usage was dominated by a mutational bias in chloroplast genomes of seed plants and that selection appeared to be limited to a subset of genes and to only subtly affect codon usage. Meantime, four, six, eight, nine, ten and 12 codons were defined as the optimal codons in chloroplast genomes of the six seed plants.
文摘Codon usage bias(CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast(cp) genes among three tea species, i.e., Camellia sinensis var. assamica(Assam tea), Camellia sinensis var. sinensis(Chinese tea) and Camellia pubicosta(wild tea species) as no work on CUB was reported earlier. To understand the patterns of codon usage among the cp genes of three tea groups, we used bioinformatic tools to investigate the protein coding sequences of cp genes. In our present study, the mean nucleobase T was the highest whereas C was the lowest in all the three tea groups. The overall AT content was more than GC content, i.e., genes were AT rich. The scaled chi-square(SCS) value indicated that the CUB of cp genes was low. The codon CGT(Arg) was over-represented in C. sinensis var. sinensis whereas GGA(Pro) was over-represented in C. pubicosta species. Heatmap study revealed that most of the GC ending codons showed positive correlations between codon usage and GC3 while AT ending codons exhibited negative correlations. From neutrality plot analysis, it was evident that natural selection had played a major role, while mutation pressure exerted a minor effect in the CUB of cp genes in three tea groups. Highly significant(P<0.01) positive correlation was found between SCS and synonymous codon usage order(SCUO) of cp genes which suggested that high expression of cp genes was associated with high degree of CUB.
基金supported by the National Natural Science Foundation of China (31401822)
文摘Apple（Malus×domestica） has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excellent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by Codon W and SPSS（Statistical Product and Service Solutions） programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also influence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple.
基金supported by the National Basic Research Program of China (2014CB138702)the National Natural Science Foundation of China (31502001)
文摘Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula. In present study, 39 531 available coding sequences （CDSs） from M. truncatula were examined for codon usage bias （CUB）. Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula, which may serve as the valuable information on genetic engineering of the model legume and forage crop.
基金Under the auspices of National Natural Science Foundation of China(No.41571146)National Natural Science Youth Foundation of China(No.51708276)Postdoctoral Science Foundation of China(No.2017M611781)
文摘Future or smart community, which mainly refers to the development of community information and communication technology(ICT) platforms or devices, has received considerable attention from urban governments and scholars. However, only a few studies have been conducted to test the actual effects of using these community ICT platforms or devices on the community satisfaction of residents. Therefore, the present study conducts a survey in 40 communities in Nanjing, China and uses a mixed linear regression model to determine the relationship between community ICT usage and community satisfaction. Results indicate that residents with high-level community ICT usage are more satisfied with their community than those with low-level community ICT usage. Moreover, evident differences are observed regarding the influence of new commodity, old commodity and affordable housing communities in Nanjing. These findings are meaningful for the construction and development of future communities.
基金The National Key R&D Program of China(No.2018YFB1600900)the Project of International Cooperation and Exchange of the National Natural Science Foundation of China(No.51561135003)the Key Project of National Natural Science Foundation of China(No.51338003)
文摘In order to study the spatiotemporal characteristics of the dockless bike sharing system(BSS)around urban rail transit stations,new normalized calculation methods are proposed to explore the temporal and spatial usage patterns of the dockless BSS around rail transit stations by using 5-weekday dockless bike sharing trip data in Nanjing,China.First,the rail transit station area(RTSA)is defined by extracting shared bike trips with trip ends falling into the area.Then,the temporal and spatial decomposition methods are developed and two criterions are calculated,namely,normalized dynamic variation of bikes(NDVB)and normalized spatial distribution of trips(NSDT).Furthermore,the temporal and spatial usage patterns are clustered and the corresponding geographical distributions of shared bikes are determined.The results show that four temporal usage patterns and two spatial patterns of dockless BSS are finally identified.Area type(urban center and suburb)has a great influence on temporal usage patterns.Spatial usage patterns are irregular and affected by limited directions,adjacent rail transit stations and street networks.The findings can help form a better understanding of dockless shared bike users behavior around rail transit stations,which will contribute to improving the service and efficiency of both rail transit and BSS.
