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DNA Marker (2):Classification of Bacteria by DNA Genetic Marker and Its Theory

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发表于 2021-2-5 17:23:10 | 显示全部楼层 |阅读模式
This is the article 1-2 in the theme 'Environmental Physiology/环境生理学' of Journal of Environment and Health Science.

2021. Copyrights Certificate Registered by Brock Chain Technology: Certificate NO. (TTAS_S.0.2_84461984181460581443119250597422911332747346) ; Certificate Verification Web: https://ttas.ntsc.ac.cn

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 2021-2-6 15:24:11 | 显示全部楼层
Article 1-2. Classification of Bacteria by DNA Genetic Marker and Its Theory/DNA遗传标记与细菌分类以及相关理论


Author: Liu Huan, MSc (First Class Honours), The University of Auckland.

However, in addition to the experiment steps discussed for virus classification, a supplementary metabolomics test is advised for further classification of bacteria families, as discussed in the article 7 of this journal, resulting in more specific classification of bacteria families related to the incidence of pathological characters. In principal, the more enzyme species variation between pathogenic bacteria families, the higher pathogenicity against the epidemiological receptors due to the higher environmental adaptiveness of pathogen families. Consequently, this methodology is listed below:

Step 1. Each bacterium is isolated from bacteria samples, and cultivated separately in situ forming a bacterium stream. Then each bacterium stream is named as stream 1, stream 2,. , stream n.

Step 2. The cytoplasm sample is abstracted in each bacterium stream labeled for subsequent step 8, and the abstracting procedure and storage of isozyme is listed in page 47 of isozyme chapter [1]. Then the chromosome sample of each bacterium stream labeled is prepared for step 2.

Step 3. The molecular cytogenetic karyotype of each bacterium stream labeled is analyzed by fluorescence in situ hybridization (FISH) technique[2] using transmission electron microscopy;

Step 4. These bacterium streams are classified by multivariate cluster analysis and genetic distance analysis on the basis of molecular cytogenetic karyotype, preliminarily leading to different families of bacteria[3];

Step 5. The optima sampling units of each bacteria family, which can well represent the genetic diversity of each bacteria family, is examined and determined as pointed out by Liu et al.,(2015) [3] for further classification based on DNA molecular marker (SSR or AFLP);

Step 6. Classification of bacteria families is further conducted on the basis of DNA molecular marker, analyzed by multivariate cluster analysis of UPGMA (unweighted pair group method with arithmetic averages) and genetic distance analysis[3];

Step 7. Gene recombination and gene mutation rate is analyzed by the inconsistence  of classification between molecular cytogenetic karyotype and DNA molecular marker[3];

Step 8. Bacteria family ‘F’ is identified by cluster analysis and genetic distance analysis based on DNA molecular markers (genotype), which results in apparent incidence of pathological characters when exposure dose to bacteria family ‘F’ increases significantly (phenotype);

Step 9. Biochemical samples are abstracted from streams of Bacteria family ‘F,’ leading to various zymogram calculated as the average similarity coefficient across different isozyme families, which is listed in the article 7 of this journal.

Step 10. Bacteria family ‘F’ is further classified into different sub-families by UPGMA (unweighted pair group method with arithmetic averages) method on the basis of the average similarity coefficient across different isozyme families between any two streams. The UPGMA calculation is listed in page 63 of isozyme chapter [1].

Step 11. Sub-Bacteria families, named as F1, F2 .... Fn, should be more specific in terms of correlation to the incidence of pathological characters.

Note: the above hypotheses and discussion about virus (in article 1-1) are also applicable on the bacteria ecosystem.The calculation of similarity coefficient between zymogram of different bacteria families is performed within one isozyme family[1]. However, this method is performed on the basis of unweighted average. Hence this article advises the steps of analyzing the zymograms with weighted average in future research:

1.If the electrophoresis pipe is the vertical one, then the horizontal bands in a pipe represent various enzyme species in an isozyme family. The bands at the same horizontal line between different pipes represent the same enzyme species, and the clearness of bands indicates activity of enzyme species (the more clearness, the higher activity of enzyme). Please note: the reproduction rate of microbial streams varies among different environmental cultivation conditions. Consequently, the density of microbial samples should be counted, ensuring the uniform concentration of microbial samples for the enzyme activity observation.

2.The whole environmental conditions (such as temperature) are simulated in situ from T1 to Tn (T1,T2,……,Tn). Within the environmental range [T1, Tn], the range of [T2, Ta] is the environmental range triggering the gene expression of enzyme species A, and the range of [T3, Tb] is the environmental range triggering the gene expression of enzyme species B,… etc. Consequently, the weight of enzyme species A is the ratio of range [T2,Ta] to the total range [T1, Tn], and the weight of enzyme species B is the ratio of range [T2, Tb] to the total range [T1,Tn],… etc. Then the similarity coefficient in one isozyme family between zymogram of different bacteria sub-families is calculated as: similarity coefficient = 2*∑(enzyme i * weight i) /
{∑(enzyme j * weight j) + ∑(enzyme k * weight k)}. In this equation, enzyme j is the enzyme species in bacteria sub-family 1 and weight j is the weight of enzyme species j; enzyme k is the enzyme species in bacteria sub-family 2 and weight k is the weight of enzyme species k; enzyme i is the common (or same) enzyme species between sub-family 1 and sub-family 2.

3.In principle, the gene expression of enzyme species A should start at the environmental condition T2 with increasing activity along the environmental gradient, and the activity should decrease after the peak value until gene expression ceases at environmental condition Ta, which can be observed by the ‘smooth’ comparison of one bacteria sub-family’ zymograms between different bacteria cultivation conditions. However, the comparison of zymograms between different sub-families should be conducted at the same environmental cultivation condition. This environmental gradient method would be the helpful indicators in the cultivation/selection of human cells or environmental microbes.


This is the revised materials in book “Proceedings for Degree of Postgraduate Diploma in Environmental Science (3rd Edition).” published in 2016. Firstly Revised on 03/01/2021; Secondly Revised on 06/02/2021.  



References:
[1]. 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.
[2]. 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).
[3]. 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.
[4]. 郑成木, 植物分子标记原理与方法, 2003, 湖南科学技术出版社.


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 楼主| 发表于 2021-2-5 17:24:15 | 显示全部楼层
Article 1-2. Classification of Bacteria by DNA Genetic Marker and Its Theory/DNA遗传标记与细菌分类以及相关理论


Author: Liu Huan, MSc (First Class Honours), The University of Auckland.

However, in addition to the experiment steps discussed for virus classification, a supplementary metabolomics test is advised for further classification of bacteria families, as discussed in the article 7 of this journal, resulting in more specific classification of bacteria families related to the incidence of pathological characters. In principal, the more enzyme species variation between pathogenic bacteria families, the higher pathogenicity against the  epidemiological receptors due to the higher environmental adaptiveness of pathogen families. Consequently, this methodology is listed below:

Step 1. Each bacterium is isolated from bacteria samples, and cultivated separately in situ forming a bacterium stream. Then each bacterium stream is named as stream 1, stream 2,. , stream n.

Step 2. The cytoplasm sample is abstracted in each bacterium stream labeled for subsequent step 8, and the abstracting procedure and storage of isozyme is listed in page 47 of isozyme chapter [1]. Then the chromosome sample of each bacterium stream labeled is prepared for step 2.

Step 3. The molecular cytogenetic karyotype of each bacterium stream labeled is analyzed by fluorescence in situ hybridization (FISH) technique[2] using transmission electron microscopy;

Step 4. These bacterium streams are classified by multivariate cluster analysis and genetic distance analysis on the basis of molecular cytogenetic karyotype, preliminarily leading to different families of bacteria[3];

Step 5. The optima sampling units of each bacteria family, which can well represent the genetic diversity of each bacteria family, is examined and determined as pointed out by Liu et al.,(2015) [3] for further classification based on DNA molecular marker (SSR or AFLP);

Step 6. Classification of bacteria families is further conducted on the basis of DNA molecular marker, analyzed by multivariate cluster analysis of UPGMA (unweighted pair group method with arithmetic averages) and genetic distance analysis[3];

Step 7. Gene recombination and gene mutation rate is analyzed by the inconsistence  of classification between molecular cytogenetic karyotype and DNA molecular marker[3];

Step 8. Bacteria family ‘F’ is identified by cluster analysis and genetic distance analysis based on DNA molecular markers (genotype), which results in apparent incidence of pathological characters when exposure dose to bacteria family ‘F’ increases significantly (phenotype);

Step 9. Biochemical samples are abstracted from streams of Bacteria family ‘F,’ leading to various zymogram calculated as the average similarity coefficient across different isozyme families, which is listed in the article 7 of this journal.

Step 10. Bacteria family ‘F’ is further classified into different sub-families by UPGMA (unweighted pair group method with arithmetic averages) method on the basis of the average similarity coefficient across different isozyme families between any two streams. The UPGMA calculation is listed in page 63 of isozyme chapter [1].

Step 11. Sub-Bacteria families, named as F1, F2 .... Fn, should be more specific in terms of correlation to the incidence of pathological characters.

Note: the above hypotheses and discussion about virus (in article 1-1) are also applicable on the bacteria ecosystem.The calculation of similarity coefficient between zymogram of different bacteria families is performed within one isozyme family[1]. However, this method is performed on the basis of unweighted average. Hence this article advises the steps of analyzing the zymograms with weighted average in future research:

1.If the electrophoresis pipe is the vertical one, then the horizontal bands in a pipe represent various enzyme species in an isozyme family. The bands at the same horizontal line between different pipes represent the same enzyme species, and the clearness of bands indicates activity of enzyme species (the more clearness, the higher activity of enzyme). Please note: the reproduction rate of microbial streams varies among different environmental cultivation conditions. Consequently, the density of microbial samples should be counted, ensuring the uniform concentration of microbial samples for the enzyme activity observation.

2.The whole environmental conditions (such as temperature) are simulated in situ from T1 to Tn (T1,T2,……,Tn). Within the environmental range [T1, Tn], the range of [T2, Ta] is the environmental range triggering the gene expression of enzyme species A, and the range of [T3, Tb] is the environmental range triggering the gene expression of enzyme species B,… etc. Consequently, the weight of enzyme species A is the ratio of range [T2,Ta] to the total range [T1, Tn], and the weight of enzyme species B is the ratio of range [T2, Tb] to the total range [T1,Tn],… etc. Then the similarity coefficient in one isozyme family between zymogram of different bacteria sub-families is calculated as: similarity coefficient = 2*∑(enzyme i * weight i) /
{∑(enzyme j * weight j) + ∑(enzyme k * weight k)}. In this equation, enzyme j is the enzyme species in bacteria sub-family 1 and weight j is the weight of enzyme species j; enzyme k is the enzyme species in bacteria sub-family 2 and weight k is the weight of enzyme species k; enzyme i is the common (or same) enzyme species between sub-family 1 and sub-family 2.

3.In principle, the gene expression of enzyme species A should start at the environmental condition T2 with increasing activity along the environmental gradient, and the activity should decrease after the peak value until gene expression ceases at environmental condition Ta, which can be observed by the ‘smooth’ comparison of one bacteria sub-family’ zymograms between different bacteria cultivation conditions. However, the comparison of zymograms between different sub-families should be conducted at the same environmental cultivation condition.


This is the revised materials in book “Proceedings for Degree of Postgraduate Diploma in Environmental Science (3rd Edition).” published in 2016. Firstly Revised on 03/01/2021; Secondly Revised on 05/02/2021.  



References:
[1]. 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.
[2]. 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).
[3]. 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.
[4]. 郑成木, 植物分子标记原理与方法, 2003, 湖南科学技术出版社.
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