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Metabolomics/新陈代谢组学

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发表于 2021-1-4 15:31:16 | 显示全部楼层 |阅读模式
This is the article 7 in the theme 'Environmental Physiology/环境生理学' of Journal of Environment and Health Science.

2016. Copyrights Register Information: The majority of these materials are registered as book '著作权人:刘焕;作品:《研究生文凭进展(第三版)》' 2016, which can be cataloged in National Copyright Database: http://qgzpdj.ccopyright.com.cn/

2016. 版权注册信息:本文大多数内容已经以图书形式登记注册在全国版权数据库,登记入库信息:著作权人:刘焕;作品:《研究生文凭进展(第三版)》 2016;可在全国版权登记数据库检索 http://qgzpdj.ccopyright.com.cn/

The formally published serials is the printing <Journal of Environment and Health Science (ISSN 2314-1628)>, and the serials NO. is the month/year when the materials accessible on this website, authorized by publisher;
正式发表的期刊是印刷版《环境与卫生科学杂志(ISSN 2314-1628)》,期刊期号为文章内容在本网站上网年/月,出版人许可自行正式发表。
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 楼主| 发表于 2021-1-5 15:22:40 | 显示全部楼层
Article 7: Metabolomics --- The Systematic Chemistry Fingerprints Between Genotype and Phenotype /新陈代谢组学---连接基因型和表现型的一项系统化学指纹识别技术


Author: Liu Huan, MSc (First Class Honours), The University of Auckland Published after graduation on data 26/08/2015


Abstract
DNA should be defined as the main carrier of material genetic information. Because cells are intelligent creatures, in addition to material genetic information, there are also memory of spirit passed on to the offspring cells in the genetic process. This has been discussed in my previous paper. After genetics, complex metabolic processes begins in cells, which can be divided into three categories in this article: primary metabolic molecules (such as tRNA), secondary metabolic biochemistry molecules (such as glutamic acid discussed in plant stress physiology), and the final metabolites (such as polysaccharide compounds). However, enzyme is the indispensable biochemicals in this metabolic process. Enzyme is the principal biochemical regulator to initiate the biochemical process of metabolism in cell biology. The primary and secondary metabolites can be significantly influenced by the cell physiological environment and genetics, whereas the cell functions constantly relies on the regulator of enzymes initiating the pathways of various metabolite process regardless of environmental changes and genetics. For example, in the previous article, it is concluded that the isozyme spectrum correspondingly to the valid antibiotics of specific pathogens must be relatively specific and unique, regardless of DNA genetics and environmental changes between different host cells. As has been discussed in previous paper, the thinking ability of multi-cellular individuals of higher intelligent is limited to three-dimension, as the thinking ability of single-cell organisms should only stay in two dimension: the recognition of bio-signals and utilization of biological enzymes. The enzyme utilization capacity can be ‘learned’ by cells. The previous paper has discussed the intelligence of cells.

Features of metabolomics in this paper:

1. Succession of study focus on the metabolic biochemistry pathways from primary metabolites to final metabolites, but choose enzymes as the indicator of metabolic reaction pathways;
2.Compared with previous enzyme spectroscopy, this article utilizes the matrix equation system to systematically analyze the cell function regulation pathway, because the environment adaptability trait of cell (such as a specific pathogen resistance) is functioned by multiple metabolic pathways to regulate a number of sub-functions, and the multiple sub-functions and pathways are not independent of each other;
3. It connects genotypes with phenotypes to distinguish which functions of cells are inherited and which need to be cultivated.

细胞结构生物中DNA分子应当准确定义为物质遗传信息的主要载体。因为细胞是有智力的,遗传过程中除了物质遗传信息,还有精神记忆机制。这在我之前的论文中已经论述。那么在此后,细胞中开始了复杂的新陈代谢过程,这里可以区分为初级代谢生化分子(如tRNA),次级代谢生化分子(如本文在植物逆境生理中论述的glutamic acid),和最终代谢生化分子(如多糖化合物)。其中不可缺少的就是酶。酶是细胞生物中对新陈代谢生化过程进行调节的首要生化指标。初级和次级代谢生化分子既可以受遗传DNA影响、也可以受细胞环境的影响而显著发生变异特性,但是细胞生理功能的调节,仅仅通过调节生物酶的合成和分泌作为生化反应链中首要途径,不管DNA先天遗传和细胞环境变化因素。比如,在本人之前文章已经论述,针对特定病原体的抗体,不管宿主细胞DNA遗传变异特性,也不管细胞环境的变化,细胞内合成针对特定病原体的有效抗体的同工酶谱都是相对唯一性和特定性。正如本文已经论述多细胞高等智慧生物的思维局限于三维思维能力,而单细胞生物的智力思维能力应该仅仅停留在识别生物信号和运用生物酶两个维度而已。而细胞生物对生物酶的识别与合成可以是后天培养的。本文已经在细胞“智慧”一文中论述了细胞的思维。

本文中新陈代谢组学的特点:
1.继承从初级代谢物到最终代谢物中对新陈代谢生化反应途径/路径作为重点研究方向,但是选择以酶作为新陈代谢反应途径的指示性指标;
2.与之前酶谱学相比,本文使用矩阵算式系统地对细胞生物功能调节途径进行分析,因为细胞环境适应性中的某一性状(比如对某一病原体实现抗病性),是由于细胞在多项功能、多个新陈代谢途径进行调节的结果,而且细胞各功能、各个新陈代谢途径之间一定是相互关联,非独立的。
3.连接了基因型和表现型,区分细胞哪些功能是先天遗传获取的,哪些功能需要后天培养的。


1.Genotype and Genetic Diversity Conservation
The feasibility of large-scale application of DNA markers on biodiversity assessment has been discussed by Liu et al.,(2014)[1]. However, the DNA markers suit not only for the classification of plant sub-populations for biodiversity assessment, but also provide the faster and convenient tool to identify the suitable plant varieties (genotype) from wild ecosystem for ecological restoration. The suitable environmental conditions for each variety growth (phenotype) can be identified by the analysis of both community and species interactions with environment as discussed by Liu et al.,(2015)[2]. According to the Environmental Standard on Classifying the Categories of Genetic Resources (HJ 626-2011) in Mainland China, three kinds of DNA  molecular methods have been listed to rank genetic resources (or endangered species) between categoryⅠand categoryⅡ, including assessment of genetic diversity, evolutionarily significant unit (ESU), or genetic contribution rate, which have been substantially discussed by Liu et al.,(2015)[2]. However, it is advised that assessment of genetic diversity would be the first choice in ranking genetic resources (or endangered species), when the total SSR primers are calculated [3]; assessment of genetic variation would be the best method to select the suitable varieties for restoration of endangered species (or other important constructive species as well), when only polymorphic SSR primers are calculated [3]. The optimalization of both sampling units and polymorphic SSR primers, which allows to well present the genetic diversity for each variety at reasonable cost, has been pointed out as well [3].

2.Metabolomics and Environmental Adaptivity
However, the supplementary test of biochemical variation in enzyme species among different varieties collected in field, as the indicator for different varieties to adjust metabolism pathways in different environmental conditions, is advised for the conclusion of environmental adaptability between genotype and phenotype (metabolomics analysis). To be more comparable, the biochemical variation in enzyme species within one isozyme family, which catalyze the same metabolism substances, is analyzed according to the similarity coefficient. The function of each isozyme family in plant resistance to different environmental stress is summarized in table 1 below, and the experiment procedure of biochemical test is listed in isozyme chapter [4].To minimize the inaccurate conclusion between genotype and phenotype, the comparison between different varieties should be conducted on the basis of bio-samples collected in the same tissue and development phase of a plant species during the same season. In principle, the higher variation in enzyme species among varieties, the better environmental adaptability for restoration. This can be attributed into two reasons: firstly, the activity of an enzyme species only responds to the specific environmental conditions, and consequently the higher enzyme species variation of an isozyme family would result in the broader environmental conditions triggering the activity of the whole isozyme family; secondly, the gene expression of an enzyme species would be regulated by the specific environmental conditions only, which also explains the higher environmental adaptivity caused by the higher enzyme species variation of an isozyme family due to the broader environmental conditions  for the regulation of gene expression as the whole isozyme family. Both reasons can result in the variation in isozyme electrophoretogram.


Table 1. The Isozyme Function in Plant Resistance to Environmental Stress (PDF Version).

The calculation of similarity coefficient between zymogram of different varieties is performed in one isozyme family[4]. However, the overall similarity coefficient among different isozyme families is calculated, on the basis of matrix for PCA analysis designed in article 10 of this journal, to reveal the systematics of environmental adaptability, as metabolomics analysis. The comparison of enzyme species variation between different seasons is required to reveal some resistance characteristics during specific environmental stress (such as cold stress). Compared with other article of this journal, the simulated environmental conditions of microbial cultivation are not suitable for botany. There are two reasons: firstly, the metabolic enzymes of botanical species is usually less sensitive to environmental conditions in comparison to microbes; secondly, the life cycle of constructive species for ecological restoration of botany communities can be hardly simulated in the controlled Lab.


3.Phenotype and Gene Mapping for Genetic Breeding
Environmental adaptivity is definitely one of the main considerations for plant genetic breeding in restoration work. Nevertheless, as discussed in other article of this journal, gene expression traits as higher environmental adaptivity are usually associated with the gene traits of lower biomass productivity (or carbon sink), which means that both gene traits would be located in the same linkage group of genome. However, as discussed in other article of this journal, the gene trait of plant drought tolerance would increase the capacity of water & soil conservation due to the advantageous partitioning for root system, which results in higher ratio of root biomass to the total biomass. For the conservation of endangered birds, the gene traits as the partitioning of more branches for habitats or suitable fruits would become the major consideration in variety selection as well. As discussed before in this journal, in comfortable conditions, the final yield of ‘suitable food’ for endangered birds should not be significantly influenced by the yield components which are mainly measured by the criteria of branches per plant individual, pods per branch, seeds per pod, and mean seed weight. This would be also explained by the theory that the sets of gene, underlying the expression as these yield component traits above, should locate in the same linkage group of genome, so that some agriculture scientists announce that the gene traits of yield components are not useful in breeding selection. However, this book hypothesizes that the gene expressed as partitioning more branches would locate in the same linkage group as some gene traits of environmental adaptivity (such as drought tolerance and higher capacity of nitrogen fixation in root system), which becomes the objectives of my future study. The infection between microbes of biological nitrogen fixation and botanical roots must be quite specific[15], so the thinner root skin, usually associated with the partitioning of more root branches, would benefit the parasitic infection of microbes, enhancing the biological nitrogen fixation in root system. Additionally, the gene trait of partitioning more branches should result in higher radiation use efficience (RUE) as well, an environmental adaptivity trait in shading side of hills. This gene trait provides not only more suitable shelters for endangered birds, but also higher sustainability of habitats for food.




This is the revised materials in book “Proceedings for Degree of Postgraduate Diploma in Environmental Science (3rd Edition).” Published in 2016. The ‘chapter’ content mentioned in this article is in previous book. Revised on 05/01/2021.


References:
[1]. Review of Conservation Genetics and Its Application on Biodiversity Monitoring and Assessment. 刘焕, 张洪初与唐秋盛, 保护遗传学方法在生物多样性监测和评价领域的应用研究. 科技视界, 2014(8). DOI: 10.3969/j.issn.2095-2457.2014.08.203
[2]. Liu, H, Ouyang T. L, Tian Chengqing (2015). Review of Evolutionary Ecology Study and Its Application on Biodiversity Monitoring and Assessment. Science & Technology Vision (6) 2015.
[3].  Liu Huan. Epidemiology        A sub-topic: Comparison between indoor and outdoor air quality at three representative sites in Auckland Center. Appendix 1. Chapter 1. In book Proceedings for Degree of Postgraduate Diploma in Environmental Science. ISBN: 978 – 988 – 12552 – 5 - 9.
[4]. 周延清, 张改娜与杨清香, 生物遗传标记与应用, 2008, 化学工业出版社.
[5].梁艳荣, 胡晓红, 张颖力, 刘湘萍(2003).植物过氧化物酶生理功能研究进展.内蒙古农业大学学报. 第 24 卷第 2 期.
[6].陈金峰, 王宫南, 程素满(2008).过氧化氢酶在植物胁迫响应中的功能研究进展.西北植物学报, 2008, 28(1):0188-0193.
[7].王晓云,毕玉芬(2006). 植物苹果酸脱氢酶研究进展.生物技术通报.2006 年第 4 期.
[8].张计育,王刚,黄胜男,宣继萍,贾晓东,郭忠仁 (2015).乙醇脱氢酶基因家族在植物抵抗非生物胁迫过程中的作用研究进展.中国农学通报2015,31(10):246-250.
[9].郝兆丰 袁进成 刘颖慧.(2012).异柠檬酸脱氢酶在植物抗氧化胁迫中的作用.生物技术通报.2012 年第 6 期.
[10]. 段昌群 王焕校.(1998).Pb+ 2、Cd+ 2、Hg+ 2对蚕豆(Vicia fabaL.)乳酸脱氢酶的影响. 生态学报.第18卷第4期.
[11].于定群,汤浩茹,张勇,罗娅,刘泽静(2012).高等植物葡萄糖-6-磷酸脱氢酶的研究进   展.July 25, 2012, 28(7): 800−812.
[12].黄国存,田波.(2001). 高等植物中的谷氨酸脱氢酶及其生理作用.植物学
通报2001,18(4):396~ 401.
[13].周滈, 杨传平, 柳参奎(2011).植物苹果酸酶在抵御逆境中的作用.第36 卷第6 期.2011年11月.
[14].杨泽峰,徐暑晖,王一凡,张恩盈,徐辰武.(2014).禾本科植物β- 淀粉酶基因家族分子进化及响应非生物胁迫的表达模式分析.科技导报2014,32(31).
[15].Liu Huan (2015). Review of Biological Control: The Population Biology of Microbial Ecosystem/种群生物学原理在微生物生态系统和生物控制技术中的应用研究(英文). Journal of Environmental & Health Science. DOI: 10.13140/RG.2.1.4219.95
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 楼主| 发表于 2021-1-4 15:32:22 | 显示全部楼层
Article 7: Conservation Genetics Strategy: Metabolomics --- The Systematic Chemistry Fingerprints Between Genotype and Phenotype /遗传资源的保护策略: 新陈代谢组学---连接基因型和表现型的一项系统化学指纹识别技术
Author: Liu Huan, MSc (First Class Honours), The University of Auckland Published after graduation on data 26/08/2015

1.Genotype and Genetic Diversity Conservation
The feasibility of large-scale application of DNA markers on biodiversity assessment has been discussed by Liu et al.,(2014)[1]. However, the DNA markers suit not only for the classification of plant sub-populations for biodiversity assessment, but also provide the faster and convenient tool to identify the suitable plant varieties (genotype) from wild ecosystem for ecological restoration. The suitable environmental conditions for each variety growth (phenotype) can be identified by the analysis of both community and species interactions with environment as discussed by Liu et al.,(2015)[2]. According to the Environmental Standard on Classifying the Categories of Genetic Resources (HJ 626-2011) in Mainland China, three kinds of DNA  molecular methods have been listed to rank genetic resources (or endangered species) between categoryⅠand categoryⅡ, including assessment of genetic diversity, evolutionarily significant unit (ESU), or genetic contribution rate, which have been substantially discussed by Liu et al.,(2015)[2]. However, it is advised that assessment of genetic diversity would be the first choice in ranking genetic resources (or endangered species), when the total SSR primers are calculated [3]; assessment of genetic variation would be the best method to select the suitable varieties for restoration of endangered species (or other important constructive species as well), when only polymorphic SSR primers are calculated [3]. The optimalization of both sampling units and polymorphic SSR primers, which allows to well  present  the genetic diversity for each variety at reasonable cost, has been pointed out as well [3].

2.Metabolomics and Environmental Adaptivity
However, the supplementary test of biochemical variation in enzyme species among different varieties collected in field, as the indicator for different varieties to adjust metabolism pathways in different environmental conditions, is advised for the conclusion of environmental adaptability between genotype and phenotype (metabolomics analysis). To be more comparable, the biochemical variation in enzyme species within one isozyme family, which catalyze the same metabolism substances, is analyzed according to the similarity coefficient. The function of each isozyme family in plant resistance to different environmental stress is summarized in table 1 below, and the experiment procedure of biochemical test is listed in isozyme chapter [4].To minimize the inaccurate conclusion between genotype and phenotype, the comparison between different varieties should be conducted on the basis of bio-samples collected in the same tissue and development phase of a plant species during the same season. In principle, the higher variation in enzyme species among varieties, the better environmental adaptability for restoration. This can be attributed into two reasons: firstly, the activity of an enzyme species only responds to the specific environmental conditions, and consequently the higher enzyme species variation of an isozyme family would result in the broader environmental conditions triggering the activity of the whole isozyme family; secondly, the gene expression of an enzyme species would be regulated by the specific environmental conditions only, which also explains the higher environmental adaptivity caused by the higher enzyme species variation of an isozyme family due to the broader environmental conditions  for the regulation of gene expression as the whole isozyme family. Both reasons can result in the variation in isozyme electrophoretogram.

Table 1. The Isozyme Function in Plant Resistance to Environmental Stress (See PDF Version).

The calculation of similarity coefficient between zymogram of different varieties is performed in one isozyme family[4]. However, the average of similarity coefficient among different isozyme families is calculated to reveal the systematics of environmental adaptability, as metabolomics analysis. The comparison of enzyme species variation between different seasons is required to reveal some resistance characteristics during specific environmental stress (such as cold stress). Compared with other article of this journal, the simulated environmental conditions of microbial cultivation are not suitable for botany. There are two reasons: firstly, the metabolic enzymes of botanical species is usually less sensitive to environmental conditions in comparison to microbes; secondly, the life cycle of constructive species for ecological

restoration of botany communities can be hardly simulated in the controlled Lab.


3.Phenotype and Gene Mapping for Genetic Breeding
Environmental adaptivity is definitely one of the main considerations for plant genetic breeding in restoration work. Nevertheless, as discussed in other article of this journal, gene expression traits as higher environmental adaptivity are usually associated with the gene traits of lower biomass productivity (or carbon sink), which means that both gene traits would be located in the same linkage group of genome. However, as discussed in other article of this journal, the gene trait of plant drought tolerance would increase the capacity of water & soil conservation due to the  advantageous partitioning for root system, which results in higher ratio of root biomass to the total biomass. For the conservation of endangered birds, the gene  traits as the partitioning of more branches for habitats or suitable fruits would become the major consideration in variety selection as well. As discussed by the appendix 1 of Chapter 4 in this book, in comfortable conditions, the final yield of ‘suitable food’ for endangered  birds should not be significantly influenced by the yield components which are mainly measured by the criteria of branches per plant individual, pods per branch, seeds per pod, and mean seed weight. This would be also explained by the theory that the sets   of gene, underlying the expression as these yield component traits above,  should locate in the same linkage group of genome, so that some agriculture scientists announce that the gene traits of yield components are not useful in breeding selection. However, this book hypothesizes that the gene expressed as partitioning more  branches would locate in the same linkage group as some gene traits of environmental adaptivity (such as drought tolerance and higher capacity of nitrogen fixation in root system), which becomes the objectives of my future study. The infection between microbes of biological nitrogen fixation and botanical roots must be quite specific[15], so the thinner root skin, usually associated with the partitioning of more root branches, would benefit the parasitic infection of microbes, enhancing the biological nitrogen fixation in root system. Additionally, the gene trait of partitioning more branches should result in higher radiation use efficience (RUE) as well, an environmental

adaptivity trait in shading side of hills. This gene trait provides not only more suitable shelters for endangered birds, but also higher sustainability of habitats for food.












































This is the revised materials in book “Proceedings for Degree of Postgraduate Diploma in Environmental Science (3rd Edition).” published in 2016. Revised on 04/01/2021.  
References:
[1]. Review of Conservation Genetics and Its Application on Biodiversity Monitoring and Assessment. 刘焕, 张洪初与唐秋盛, 保护遗传学方法在生物多样性监测和评价领域的应用研究. 科技视界, 2014(8). DOI: 10.3969/j.issn.2095-2457.2014.08.203
[2]. Liu, H, Ouyang T. L, Tian Chengqing (2015). Review of Evolutionary Ecology Study and Its Application on Biodiversity Monitoring and Assessment. Science & Technology Vision (6) 2015.
[3].  Liu Huan. Epidemiology        A sub-topic: Comparison between indoor and outdoor air quality at
three representative sites in Auckland Center. Appendix 1. Chapter 1. In book Proceedings for Degree of Postgraduate Diploma in Environmental Science. ISBN: 978 – 988 – 12552 – 5 - 9.
[4]. 周延清, 张改娜与杨清香, 生物遗传标记与应用, 2008, 化学工业出版社.
[5].梁艳荣, 胡晓红, 张颖力, 刘湘萍(2003).植物过氧化物酶生理功能研究进展.内蒙古农业大学学报. 第 24 卷第 2 期.
[6].陈金峰, 王宫南, 程素满(2008).过氧化氢酶在植物胁迫响应中的功能研究进展.西北植物学报, 2008, 28(1):0188-0193.
[7].王晓云,毕玉芬(2006). 植物苹果酸脱氢酶研究进展.生物技术通报.2006 年第 4 期.
[8].张计育,王刚,黄胜男,宣继萍,贾晓东,郭忠仁 (2015).乙醇脱氢酶基因家族在植物抵抗非生物胁迫过程中的作用研究进展.中国农学通报2015,31(10):246-250.
[9].郝兆丰 袁进成 刘颖慧.(2012).异柠檬酸脱氢酶在植物抗氧化胁迫中的作用.生物技术通报.2012 年第 6 期.
[10]. 段昌群 王焕校.(1998).Pb+ 2、Cd+ 2、Hg+ 2对蚕豆(Vicia fabaL.)乳酸脱氢酶的影响. 生态学报.第18卷第4期.
[11].于定群,汤浩茹,张勇,罗娅,刘泽静(2012).高等植物葡萄糖-6-磷酸脱氢酶的研究进   展.July 25, 2012, 28(7): 800−812.
[12].黄国存,田波.(2001). 高等植物中的谷氨酸脱氢酶及其生理作用.植物学
通报2001,18(4):396~ 401.
[13].周滈, 杨传平, 柳参奎(2011).植物苹果酸酶在抵御逆境中的作用.第36 卷第6 期.2011年11月.
[14].杨泽峰,徐暑晖,王一凡,张恩盈,徐辰武.(2014).禾本科植物β- 淀粉酶基因家族分子进化及响应非生物胁迫的表达模式分析.科技导报2014,32(31).
[15].Liu Huan (2015). Review of Biological Control: The Population Biology of Microbial
Ecosystem/种群生物学原理在微生物生态系统和生物控制技术中的应用研究(英文). Journal of Environmental & Health Science. DOI: 10.13140/RG.2.1.4219.95
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 楼主| 发表于 2021-1-5 09:34:26 | 显示全部楼层
Article 7: Metabolomics --- The Systematic Chemistry Fingerprints Between Genotype and Phenotype /新陈代谢组学---连接基因型和表现型的一项系统化学指纹识别技术
Author: Liu Huan, MSc (First Class Honours), The University of Auckland Published after graduation on data 26/08/2015

1.Genotype and Genetic Diversity Conservation
The feasibility of large-scale application of DNA markers on biodiversity assessment has been discussed by Liu et al.,(2014)[1]. However, the DNA markers suit not only for the classification of plant sub-populations for biodiversity assessment, but also provide the faster and convenient tool to identify the suitable plant varieties (genotype) from wild ecosystem for ecological restoration. The suitable environmental conditions for each variety growth (phenotype) can be identified by the analysis of both community and species interactions with environment as discussed by Liu et al.,(2015)[2]. According to the Environmental Standard on Classifying the Categories of Genetic Resources (HJ 626-2011) in Mainland China, three kinds of DNA  molecular methods have been listed to rank genetic resources (or endangered species) between categoryⅠand categoryⅡ, including assessment of genetic diversity, evolutionarily significant unit (ESU), or genetic contribution rate, which have been substantially discussed by Liu et al.,(2015)[2]. However, it is advised that assessment of genetic diversity would be the first choice in ranking genetic resources (or endangered species), when the total SSR primers are calculated [3]; assessment of genetic variation would be the best method to select the suitable varieties for restoration of endangered species (or other important constructive species as well), when only polymorphic SSR primers are calculated [3]. The optimalization of both sampling units and polymorphic SSR primers, which allows to well  present  the genetic diversity for each variety at reasonable cost, has been pointed out as well [3].

2.Metabolomics and Environmental Adaptivity
However, the supplementary test of biochemical variation in enzyme species among different varieties collected in field, as the indicator for different varieties to adjust metabolism pathways in different environmental conditions, is advised for the conclusion of environmental adaptability between genotype and phenotype (metabolomics analysis). To be more comparable, the biochemical variation in enzyme species within one isozyme family, which catalyze the same metabolism substances, is analyzed according to the similarity coefficient. The function of each isozyme family in plant resistance to different environmental stress is summarized in table 1 below, and the experiment procedure of biochemical test is listed in isozyme chapter [4].To minimize the inaccurate conclusion between genotype and phenotype, the comparison between different varieties should be conducted on the basis of bio-samples collected in the same tissue and development phase of a plant species during the same season. In principle, the higher variation in enzyme species among varieties, the better environmental adaptability for restoration. This can be attributed into two reasons: firstly, the activity of an enzyme species only responds to the specific environmental conditions, and consequently the higher enzyme species variation of an isozyme family would result in the broader environmental conditions triggering the activity of the whole isozyme family; secondly, the gene expression of an enzyme species would be regulated by the specific environmental conditions only, which also explains the higher environmental adaptivity caused by the higher enzyme species variation of an isozyme family due to the broader environmental conditions  for the regulation of gene expression as the whole isozyme family. Both reasons can result in the variation in isozyme electrophoretogram.

Table 1. The Isozyme Function in Plant Resistance to Environmental Stress (PDF Version).

The calculation of similarity coefficient between zymogram of different varieties is performed in one isozyme family[4]. However, the average of similarity coefficient among different isozyme families is calculated to reveal the systematics of environmental adaptability, as metabolomics analysis. The comparison of enzyme species variation between different seasons is required to reveal some resistance characteristics during specific environmental stress (such as cold stress). Compared with other article of this journal, the simulated environmental conditions of microbial cultivation are not suitable for botany. There are two reasons: firstly, the metabolic enzymes of botanical species is usually less sensitive to environmental conditions in comparison to microbes; secondly, the life cycle of constructive species for ecological

restoration of botany communities can be hardly simulated in the controlled Lab.


3.Phenotype and Gene Mapping for Genetic Breeding
Environmental adaptivity is definitely one of the main considerations for plant genetic breeding in restoration work. Nevertheless, as discussed in other article of this journal, gene expression traits as higher environmental adaptivity are usually associated with the gene traits of lower biomass productivity (or carbon sink), which means that both gene traits would be located in the same linkage group of genome. However, as discussed in other article of this journal, the gene trait of plant drought tolerance would increase the capacity of water & soil conservation due to the advantageous partitioning for root system, which results in higher ratio of root biomass to the total biomass. For the conservation of endangered birds, the gene traits as the partitioning of more branches for habitats or suitable fruits would become the major consideration in variety selection as well. As discussed before in this journal, in comfortable conditions, the final yield of ‘suitable food’ for endangered birds should not be significantly influenced by the yield components which are mainly measured by the criteria of branches per plant individual, pods per branch, seeds per pod, and mean seed weight. This would be also explained by the theory that the sets of gene, underlying the expression as these yield component traits above, should locate in the same linkage group of genome, so that some agriculture scientists announce that the gene traits of yield components are not useful in breeding selection. However, this book hypothesizes that the gene expressed as partitioning more branches would locate in the same linkage group as some gene traits of environmental adaptivity (such as drought tolerance and higher capacity of nitrogen fixation in root system), which becomes the objectives of my future study. The infection between microbes of biological nitrogen fixation and botanical roots must be quite specific[15], so the thinner root skin, usually associated with the partitioning of more root branches, would benefit the parasitic infection of microbes, enhancing the biological nitrogen fixation in root system. Additionally, the gene trait of partitioning more branches should result in higher radiation use efficience (RUE) as well, an environmental
adaptivity trait in shading side of hills. This gene trait provides not only more suitable shelters for endangered birds, but also higher sustainability of habitats for food.



Conclusion:
DNA should be defined as the main carrier of material genetic information. Because cells are intelligent creatures, in addition to material genetic information, there are also memory of spirit passed on to the offspring cells in the genetic process. This has been discussed in my previous paper. After genetics, complex metabolic processes begins in cells, which can be divided into three categories in this article: primary metabolic molecules (such as tRNA), secondary metabolic biochemistry molecules (such as glutamic acid discussed in plant stress physiology), and the final metabolites (such as polysaccharide compounds). However, enzyme is the indispensable biochemicals in this metabolic process. Enzyme is the principal biochemical regulator to initiate the biochemical process of metabolism in cell biology. The primary and secondary metabolites can be significantly influenced by the cell physiological environment and genetics, whereas the cell functions constantly relies on the regulator of enzymes initiating the pathways of various metabolite process regardless of environmental changes and genetics. For example, in the previous article, it is concluded that the isozyme spectrum correspondingly to the valid antibiotics of specific pathogens must be relatively specific and unique, regardless of DNA genetics and environmental changes between different host cells. As has been discussed in previous paper, the thinking ability of multi-cellular individuals of higher intelligent is limited to three-dimension, as the thinking ability of single-cell organisms should only stay in two dimension: the recognition of bio-signals and utilization of biological enzymes. The enzyme utilization capacity can be ‘learned’ by cells. The previous paper has discussed the intelligence of cells.

细胞结构生物中DNA分子应当准确定义为物质遗传信息的主要载体。因为细胞是有智力的,遗传过程中除了物质遗传信息,还有精神记忆机制。这在我之前的论文中已经论述。那么在此后,细胞中开始了复杂的新陈代谢过程,这里可以区分为初级代谢生化分子(如tRNA),次级代谢生化分子(如本文在植物逆境生理中论述的glutamic acid),和最终代谢生化分子(如多糖化合物)。其中不可缺少的就是酶。酶是细胞生物中对新陈代谢生化过程进行调节的首要生化指标。初级和次级代谢生化分子既可以受遗传DNA影响、也可以受细胞环境的影响而显著发生变异特性,但是细胞生理功能的调节,仅仅通过调节生物酶的合成和分泌作为生化反应链中首要途径,不管DNA先天遗传和细胞环境变化因素。比如,在本人之前文章已经论述,针对特定病原体的抗体,不管宿主细胞DNA遗传变异特性,也不管细胞环境的变化,细胞内合成针对特定病原体的有效抗体的同工酶谱都是相对唯一性和特定性。正如本文已经论述多细胞高等智慧生物的思维局限于三维思维能力,而单细胞生物的智力思维能力应该仅仅停留在识别生物信号和运用生物酶两个维度而已。而细胞生物对生物酶的识别与合成可以是后天培养的。本文已经在细胞“智慧”一文中论述了细胞的思维。



























This is the revised materials in book “Proceedings for Degree of Postgraduate Diploma in Environmental Science (3rd Edition).” published in 2016. Revised on 04/01/2021.  
References:
[1]. Review of Conservation Genetics and Its Application on Biodiversity Monitoring and Assessment. 刘焕, 张洪初与唐秋盛, 保护遗传学方法在生物多样性监测和评价领域的应用研究. 科技视界, 2014(8). DOI: 10.3969/j.issn.2095-2457.2014.08.203
[2]. Liu, H, Ouyang T. L, Tian Chengqing (2015). Review of Evolutionary Ecology Study and Its Application on Biodiversity Monitoring and Assessment. Science & Technology Vision (6) 2015.
[3].  Liu Huan. Epidemiology        A sub-topic: Comparison between indoor and outdoor air quality at
three representative sites in Auckland Center. Appendix 1. Chapter 1. In book Proceedings for Degree of Postgraduate Diploma in Environmental Science. ISBN: 978 – 988 – 12552 – 5 - 9.
[4]. 周延清, 张改娜与杨清香, 生物遗传标记与应用, 2008, 化学工业出版社.
[5].梁艳荣, 胡晓红, 张颖力, 刘湘萍(2003).植物过氧化物酶生理功能研究进展.内蒙古农业大学学报. 第 24 卷第 2 期.
[6].陈金峰, 王宫南, 程素满(2008).过氧化氢酶在植物胁迫响应中的功能研究进展.西北植物学报, 2008, 28(1):0188-0193.
[7].王晓云,毕玉芬(2006). 植物苹果酸脱氢酶研究进展.生物技术通报.2006 年第 4 期.
[8].张计育,王刚,黄胜男,宣继萍,贾晓东,郭忠仁 (2015).乙醇脱氢酶基因家族在植物抵抗非生物胁迫过程中的作用研究进展.中国农学通报2015,31(10):246-250.
[9].郝兆丰 袁进成 刘颖慧.(2012).异柠檬酸脱氢酶在植物抗氧化胁迫中的作用.生物技术通报.2012 年第 6 期.
[10]. 段昌群 王焕校.(1998).Pb+ 2、Cd+ 2、Hg+ 2对蚕豆(Vicia fabaL.)乳酸脱氢酶的影响. 生态学报.第18卷第4期.
[11].于定群,汤浩茹,张勇,罗娅,刘泽静(2012).高等植物葡萄糖-6-磷酸脱氢酶的研究进   展.July 25, 2012, 28(7): 800−812.
[12].黄国存,田波.(2001). 高等植物中的谷氨酸脱氢酶及其生理作用.植物学
通报2001,18(4):396~ 401.
[13].周滈, 杨传平, 柳参奎(2011).植物苹果酸酶在抵御逆境中的作用.第36 卷第6 期.2011年11月.
[14].杨泽峰,徐暑晖,王一凡,张恩盈,徐辰武.(2014).禾本科植物β- 淀粉酶基因家族分子进化及响应非生物胁迫的表达模式分析.科技导报2014,32(31).
[15].Liu Huan (2015). Review of Biological Control: The Population Biology of Microbial
Ecosystem/种群生物学原理在微生物生态系统和生物控制技术中的应用研究(英文). Journal of Environmental & Health Science. DOI: 10.13140/RG.2.1.4219.95
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 楼主| 发表于 2021-1-5 11:20:55 | 显示全部楼层
Article 7: Metabolomics --- The Systematic Chemistry Fingerprints Between Genotype and Phenotype /新陈代谢组学---连接基因型和表现型的一项系统化学指纹识别技术
Author: Liu Huan, MSc (First Class Honours), The University of Auckland Published after graduation on data 26/08/2015

1.Genotype and Genetic Diversity Conservation
The feasibility of large-scale application of DNA markers on biodiversity assessment has been discussed by Liu et al.,(2014)[1]. However, the DNA markers suit not only for the classification of plant sub-populations for biodiversity assessment, but also provide the faster and convenient tool to identify the suitable plant varieties (genotype) from wild ecosystem for ecological restoration. The suitable environmental conditions for each variety growth (phenotype) can be identified by the analysis of both community and species interactions with environment as discussed by Liu et al.,(2015)[2]. According to the Environmental Standard on Classifying the Categories of Genetic Resources (HJ 626-2011) in Mainland China, three kinds of DNA  molecular methods have been listed to rank genetic resources (or endangered species) between categoryⅠand categoryⅡ, including assessment of genetic diversity, evolutionarily significant unit (ESU), or genetic contribution rate, which have been substantially discussed by Liu et al.,(2015)[2]. However, it is advised that assessment of genetic diversity would be the first choice in ranking genetic resources (or endangered species), when the total SSR primers are calculated [3]; assessment of genetic variation would be the best method to select the suitable varieties for restoration of endangered species (or other important constructive species as well), when only polymorphic SSR primers are calculated [3]. The optimalization of both sampling units and polymorphic SSR primers, which allows to well  present  the genetic diversity for each variety at reasonable cost, has been pointed out as well [3].

2.Metabolomics and Environmental Adaptivity
However, the supplementary test of biochemical variation in enzyme species among different varieties collected in field, as the indicator for different varieties to adjust metabolism pathways in different environmental conditions, is advised for the conclusion of environmental adaptability between genotype and phenotype (metabolomics analysis). To be more comparable, the biochemical variation in enzyme species within one isozyme family, which catalyze the same metabolism substances, is analyzed according to the similarity coefficient. The function of each isozyme family in plant resistance to different environmental stress is summarized in table 1 below, and the experiment procedure of biochemical test is listed in isozyme chapter [4].To minimize the inaccurate conclusion between genotype and phenotype, the comparison between different varieties should be conducted on the basis of bio-samples collected in the same tissue and development phase of a plant species during the same season. In principle, the higher variation in enzyme species among varieties, the better environmental adaptability for restoration. This can be attributed into two reasons: firstly, the activity of an enzyme species only responds to the specific environmental conditions, and consequently the higher enzyme species variation of an isozyme family would result in the broader environmental conditions triggering the activity of the whole isozyme family; secondly, the gene expression of an enzyme species would be regulated by the specific environmental conditions only, which also explains the higher environmental adaptivity caused by the higher enzyme species variation of an isozyme family due to the broader environmental conditions  for the regulation of gene expression as the whole isozyme family. Both reasons can result in the variation in isozyme electrophoretogram.

Table 1. The Isozyme Function in Plant Resistance to Environmental Stress (PDF Version).

The calculation of similarity coefficient between zymogram of different varieties is performed in one isozyme family[4]. However, the average of similarity coefficient among different isozyme families is calculated to reveal the systematics of environmental adaptability, as metabolomics analysis. The comparison of enzyme species variation between different seasons is required to reveal some resistance characteristics during specific environmental stress (such as cold stress). Compared with other article of this journal, the simulated environmental conditions of microbial cultivation are not suitable for botany. There are two reasons: firstly, the metabolic enzymes of botanical species is usually less sensitive to environmental conditions in comparison to microbes; secondly, the life cycle of constructive species for ecological

restoration of botany communities can be hardly simulated in the controlled Lab.


3.Phenotype and Gene Mapping for Genetic Breeding
Environmental adaptivity is definitely one of the main considerations for plant genetic breeding in restoration work. Nevertheless, as discussed in other article of this journal, gene expression traits as higher environmental adaptivity are usually associated with the gene traits of lower biomass productivity (or carbon sink), which means that both gene traits would be located in the same linkage group of genome. However, as discussed in other article of this journal, the gene trait of plant drought tolerance would increase the capacity of water & soil conservation due to the advantageous partitioning for root system, which results in higher ratio of root biomass to the total biomass. For the conservation of endangered birds, the gene traits as the partitioning of more branches for habitats or suitable fruits would become the major consideration in variety selection as well. As discussed before in this journal, in comfortable conditions, the final yield of ‘suitable food’ for endangered birds should not be significantly influenced by the yield components which are mainly measured by the criteria of branches per plant individual, pods per branch, seeds per pod, and mean seed weight. This would be also explained by the theory that the sets of gene, underlying the expression as these yield component traits above, should locate in the same linkage group of genome, so that some agriculture scientists announce that the gene traits of yield components are not useful in breeding selection. However, this book hypothesizes that the gene expressed as partitioning more branches would locate in the same linkage group as some gene traits of environmental adaptivity (such as drought tolerance and higher capacity of nitrogen fixation in root system), which becomes the objectives of my future study. The infection between microbes of biological nitrogen fixation and botanical roots must be quite specific[15], so the thinner root skin, usually associated with the partitioning of more root branches, would benefit the parasitic infection of microbes, enhancing the biological nitrogen fixation in root system. Additionally, the gene trait of partitioning more branches should result in higher radiation use efficience (RUE) as well, an environmental adaptivity trait in shading side of hills. This gene trait provides not only more suitable shelters for endangered birds, but also higher sustainability of habitats for food.


Conclusion:
DNA should be defined as the main carrier of material genetic information. Because cells are intelligent creatures, in addition to material genetic information, there are also memory of spirit passed on to the offspring cells in the genetic process. This has been discussed in my previous paper. After genetics, complex metabolic processes begins in cells, which can be divided into three categories in this article: primary metabolic molecules (such as tRNA), secondary metabolic biochemistry molecules (such as glutamic acid discussed in plant stress physiology), and the final metabolites (such as polysaccharide compounds). However, enzyme is the indispensable biochemicals in this metabolic process. Enzyme is the principal biochemical regulator to initiate the biochemical process of metabolism in cell biology. The primary and secondary metabolites can be significantly influenced by the cell physiological environment and genetics, whereas the cell functions constantly relies on the regulator of enzymes initiating the pathways of various metabolite process regardless of environmental changes and genetics. For example, in the previous article, it is concluded that the isozyme spectrum correspondingly to the valid antibiotics of specific pathogens must be relatively specific and unique, regardless of DNA genetics and environmental changes between different host cells. As has been discussed in previous paper, the thinking ability of multi-cellular individuals of higher intelligent is limited to three-dimension, as the thinking ability of single-cell organisms should only stay in two dimension: the recognition of bio-signals and utilization of biological enzymes. The enzyme utilization capacity can be ‘learned’ by cells. The previous paper has discussed the intelligence of cells.

Features of metabolomics in this paper:

1. Succession of study focus on the metabolic biochemistry pathways from primary metabolites to final metabolites, but choose enzymes as the indicator of metabolic reaction pathways;
2.Compared with previous enzyme spectroscopy, this article utilizes the matrix equation system to systematically analyze the cell function regulation pathway, because the environment adaptability trait of cell (such as a specific pathogen resistance) is functioned by multiple metabolic pathways to regulate a number of sub-functions, and the multiple sub-functions and pathways are not independent of each other;
3. It connects genotypes with phenotypes to distinguish which functions of cells are inherited and which need to be cultivated.

细胞结构生物中DNA分子应当准确定义为物质遗传信息的主要载体。因为细胞是有智力的,遗传过程中除了物质遗传信息,还有精神记忆机制。这在我之前的论文中已经论述。那么在此后,细胞中开始了复杂的新陈代谢过程,这里可以区分为初级代谢生化分子(如tRNA),次级代谢生化分子(如本文在植物逆境生理中论述的glutamic acid),和最终代谢生化分子(如多糖化合物)。其中不可缺少的就是酶。酶是细胞生物中对新陈代谢生化过程进行调节的首要生化指标。初级和次级代谢生化分子既可以受遗传DNA影响、也可以受细胞环境的影响而显著发生变异特性,但是细胞生理功能的调节,仅仅通过调节生物酶的合成和分泌作为生化反应链中首要途径,不管DNA先天遗传和细胞环境变化因素。比如,在本人之前文章已经论述,针对特定病原体的抗体,不管宿主细胞DNA遗传变异特性,也不管细胞环境的变化,细胞内合成针对特定病原体的有效抗体的同工酶谱都是相对唯一性和特定性。正如本文已经论述多细胞高等智慧生物的思维局限于三维思维能力,而单细胞生物的智力思维能力应该仅仅停留在识别生物信号和运用生物酶两个维度而已。而细胞生物对生物酶的识别与合成可以是后天培养的。本文已经在细胞“智慧”一文中论述了细胞的思维。

本文中新陈代谢组学的特点:
1.继承从初级代谢物到最终代谢物中对新陈代谢生化反应途径/路径作为重点研究方向,但是选择以酶作为新陈代谢反应途径的指示性指标;
2.与之前酶谱学相比,本文使用矩阵算式系统地对细胞生物功能调节途径进行分析,因为细胞环境适应性中的某一性状(比如对某一病原体实现抗病性),是由于细胞在多项功能、多个新陈代谢途径进行调节的结果,而且细胞各功能、各个新陈代谢途径之间一定是相互关联,非独立的。
3.连接了基因型和表现型,区分细胞哪些功能是先天遗传获取的,哪些功能需要后天培养的。




























































This is the revised materials in book “Proceedings for Degree of Postgraduate Diploma in Environmental Science (3rd Edition).” published in 2016. Revised on 04/01/2021.  
References:
[1]. Review of Conservation Genetics and Its Application on Biodiversity Monitoring and Assessment. 刘焕, 张洪初与唐秋盛, 保护遗传学方法在生物多样性监测和评价领域的应用研究. 科技视界, 2014(8). DOI: 10.3969/j.issn.2095-2457.2014.08.203
[2]. Liu, H, Ouyang T. L, Tian Chengqing (2015). Review of Evolutionary Ecology Study and Its Application on Biodiversity Monitoring and Assessment. Science & Technology Vision (6) 2015.
[3].  Liu Huan. Epidemiology        A sub-topic: Comparison between indoor and outdoor air quality at
three representative sites in Auckland Center. Appendix 1. Chapter 1. In book Proceedings for Degree of Postgraduate Diploma in Environmental Science. ISBN: 978 – 988 – 12552 – 5 - 9.
[4]. 周延清, 张改娜与杨清香, 生物遗传标记与应用, 2008, 化学工业出版社.
[5].梁艳荣, 胡晓红, 张颖力, 刘湘萍(2003).植物过氧化物酶生理功能研究进展.内蒙古农业大学学报. 第 24 卷第 2 期.
[6].陈金峰, 王宫南, 程素满(2008).过氧化氢酶在植物胁迫响应中的功能研究进展.西北植物学报, 2008, 28(1):0188-0193.
[7].王晓云,毕玉芬(2006). 植物苹果酸脱氢酶研究进展.生物技术通报.2006 年第 4 期.
[8].张计育,王刚,黄胜男,宣继萍,贾晓东,郭忠仁 (2015).乙醇脱氢酶基因家族在植物抵抗非生物胁迫过程中的作用研究进展.中国农学通报2015,31(10):246-250.
[9].郝兆丰 袁进成 刘颖慧.(2012).异柠檬酸脱氢酶在植物抗氧化胁迫中的作用.生物技术通报.2012 年第 6 期.
[10]. 段昌群 王焕校.(1998).Pb+ 2、Cd+ 2、Hg+ 2对蚕豆(Vicia fabaL.)乳酸脱氢酶的影响. 生态学报.第18卷第4期.
[11].于定群,汤浩茹,张勇,罗娅,刘泽静(2012).高等植物葡萄糖-6-磷酸脱氢酶的研究进   展.July 25, 2012, 28(7): 800−812.
[12].黄国存,田波.(2001). 高等植物中的谷氨酸脱氢酶及其生理作用.植物学
通报2001,18(4):396~ 401.
[13].周滈, 杨传平, 柳参奎(2011).植物苹果酸酶在抵御逆境中的作用.第36 卷第6 期.2011年11月.
[14].杨泽峰,徐暑晖,王一凡,张恩盈,徐辰武.(2014).禾本科植物β- 淀粉酶基因家族分子进化及响应非生物胁迫的表达模式分析.科技导报2014,32(31).
[15].Liu Huan (2015). Review of Biological Control: The Population Biology of Microbial
Ecosystem/种群生物学原理在微生物生态系统和生物控制技术中的应用研究(英文). Journal of Environmental & Health Science. DOI: 10.13140/RG.2.1.4219.95

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