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 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
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
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
[目的/意义]对比分析相同主题的不同类型科学文献的使用行为,利用用户学术行为数据全面测评学术论文影响力。[方法/过程]基于Web of Science数据库中学术论文使用次数,分析比较不同学科文献的使用差异。从文献使用入手,收集2013-2017年3...[目的/意义]对比分析相同主题的不同类型科学文献的使用行为,利用用户学术行为数据全面测评学术论文影响力。[方法/过程]基于Web of Science数据库中学术论文使用次数,分析比较不同学科文献的使用差异。从文献使用入手,收集2013-2017年3D打印领域的论文数据,以化学、工程文献为对比分析对象,从论文的学科视角分析使用次数与被引频次之间的相关性,分析高使用与高引用(Top 10%)论文的重合文献,探测文献使用差异,并进行独立样本T检验。[结果/结论]U1与被引次数成微弱正相关,U2与被引次数显著性相关;两学科的科学论文在使用上存在统计学意义上的显著差异,可能原因是不同学科学者的文献使用行为不同。此外,文献类型对使用次数有影响,综述类文献信息量较为丰富,从而可以获得更多的使用、引用。展开更多
新型数据的涌现一直是推动信息计量学前行的重要动力,Web of Science(Wo S)给出的学术文献用量级数据Usage可望在影响力维度、学科差异、行为动机三个理论方面为引文分析提供补充视角。本研究以2013年物理学、计算机、经济学和图书情报...新型数据的涌现一直是推动信息计量学前行的重要动力,Web of Science(Wo S)给出的学术文献用量级数据Usage可望在影响力维度、学科差异、行为动机三个理论方面为引文分析提供补充视角。本研究以2013年物理学、计算机、经济学和图书情报学被SCI和SSCI收录的166 767篇论文为研究样本,探索性地研究了该Usage数据的测度特征。结果显示,相较于引文数据,Usage更具测评区分度与敏感性;其在高频局部呈现出近似正偏态分布,于累积整体涌现出近似幂律分布;Usage的测评结果具有独立性,且与引文结果没有本质对立。虽然Wo S平台的Usage仍有笼统性、可伪性和封闭性之局限,但仍不失为配合引文数据、提供丰富影响力测评视域的可能选择之一。图4。表6。参考文献23。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
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
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
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 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
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
在经济全球化背景下,出于贸易交流、文化传播等活动的需要,世界语言—英语被广泛学习。各国语言学家粗略地把英语分为英国英语和美国英语两大变体。因为美国的强国地位及其好莱坞效应,美国英语在各种场合较之英国英语被更广泛使用。而...在经济全球化背景下,出于贸易交流、文化传播等活动的需要,世界语言—英语被广泛学习。各国语言学家粗略地把英语分为英国英语和美国英语两大变体。因为美国的强国地位及其好莱坞效应,美国英语在各种场合较之英国英语被更广泛使用。而在与美国接壤的加拿大,一直被语言学家定义为以英国英语为基础,受美国英语强烈影响的加拿大英语仍在全球化背景下保持着自己的语言特色。文章通过对Guide to Canadian English Usage(第二版)的解析,粗略列举加拿大英语中现存的特色词汇并与英、美英语进行比较、分析。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
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.
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[目的/意义]对比分析相同主题的不同类型科学文献的使用行为,利用用户学术行为数据全面测评学术论文影响力。[方法/过程]基于Web of Science数据库中学术论文使用次数,分析比较不同学科文献的使用差异。从文献使用入手,收集2013-2017年3D打印领域的论文数据,以化学、工程文献为对比分析对象,从论文的学科视角分析使用次数与被引频次之间的相关性,分析高使用与高引用(Top 10%)论文的重合文献,探测文献使用差异,并进行独立样本T检验。[结果/结论]U1与被引次数成微弱正相关,U2与被引次数显著性相关;两学科的科学论文在使用上存在统计学意义上的显著差异,可能原因是不同学科学者的文献使用行为不同。此外,文献类型对使用次数有影响,综述类文献信息量较为丰富,从而可以获得更多的使用、引用。
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.
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.
文摘在经济全球化背景下,出于贸易交流、文化传播等活动的需要,世界语言—英语被广泛学习。各国语言学家粗略地把英语分为英国英语和美国英语两大变体。因为美国的强国地位及其好莱坞效应,美国英语在各种场合较之英国英语被更广泛使用。而在与美国接壤的加拿大,一直被语言学家定义为以英国英语为基础,受美国英语强烈影响的加拿大英语仍在全球化背景下保持着自己的语言特色。文章通过对Guide to Canadian English Usage(第二版)的解析,粗略列举加拿大英语中现存的特色词汇并与英、美英语进行比较、分析。
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.