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Metabolomics (4-1):Metebolomics and Immunology Cultivation/新陈代谢组学之4-1

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发表于 2021-2-7 11:03:00 | 显示全部楼层 |阅读模式
This is the article 10-1 in the theme 'Environmental Physiology/环境生理学' of Journal of Environment and Health Science.

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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/

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 楼主| 发表于 2021-2-7 11:04:43 | 显示全部楼层

Article 10: Metebolomics and Immunology Cultivation /新陈代谢组学与免疫力培养

Author: Liu Huan, MSc (First Class Honours), The University of Auckland.
Published after graduation on 11/01/2016, Revised on 06/02/2021.

Methods:

The same strain of microbes is divided into two samples for the bio-signal simulation:
1.There are two kinds of cultivation conditions simulated in Lab for microbe reproduction process: one is the ‘comfortable’ condition (Sample 1); the other is under UV-B radiation for cultivation (Sample 2). The microbe samples are collected after sufficient reproduction process (Ten generations).
2.After sufficient reproduction process, the UV-B radiation simulation stops. Then both sample 1 and sample 2 are separately transferred into moisture simulation process: different moisture conditions of microbial cultivation are simulated in Lab, and labeled as T1, T2, ..., Tn.
3.Metabolomics tests are conducted (listed by the appendix 2 in Chapter 1 of this book) after moisture simulation of T1, T2, ..., Tn respectively, resulting in different zymograms as: M1, M2, ..., Mn.
4.Each isozyme family is labeled as 1, 2, 3..., and E; It is hypothesized that the bands at the same line across different isozyme families are the enzyme species at the same locus, named as enzyme ‘species i’ (i = 1, 2, ..., I), and each isozyme family has the same amount (I) of enzyme species (Please note: this is different from the identification of real enzyme species in the appendix 2 of chapter 1). Then there is a 3-dimension (I× E × N) matrix presented in this research. I is the total amount of enzyme species within a isozyme family; E is the total amount of isozyme families; N is the total amount of zymograms among different simulated moisture conditions:


X= │Xien │( i = 1, 2, ....I; e = 1, 2, .... E; n= 1, 2, ... N)
Xien is the occurrence of enzyme ‘species i’ in the isozyme ‘family e’ during simulated moisture condition Tn. The value of Xien is one or zero.


Matrix Se = Xe × (Xe)T Xe = │Xin│( i = 1, 2, ....I; n= 1, 2, ... N); (Xe)T is the transpose of the matrix Xe (Matrix is shown in PDF Version):

The Principal Components Analysis (PCA) method of matrix X is specified [1]. PCA is firstly conducted on the basis of matrix Se, revealing the biochemical dynamics of a isozyme ‘family e’ among different simulated moisture conditions. In matrix Se, it is hypothesized that the variable in PCA represents the biochemistry dynamics of each enzyme ‘species i’.

S = ΣSe (e = 1, 2, E)

PCA is further conducted on the basis of matrix S, revealing the biochemical dynamics among different isozyme families over the whole simulated moisture conditions. In matrix S, it is hypothesized that the variable in PCA represents the biochemistry dynamics of each enzyme ‘species i’ across all the isozyme families.

However, for the comparison between sample 1 and sample 2, this book need to present more procedures for subsequent analysis: in matrix Se, the biochemistry

dynamics of the first three enzyme species, which reveal the most differences in the total variation by PCA in an isozyme family, are selected for comparison between sample 1 and sample 2; in matrix S, the biochemistry dynamics of the first three enzyme species, which reveal the most differences in the total variation by PCA  across all the isozyme families, are selected for comparison between sample 1 and sample 2; the sum dynamics of the first three enzyme species in a isozyme family (= the sum Variance Contribution Ratio (VCR) of the first three enzyme species  in matrix Se), represents the total variation of a isozyme family over the whole simulated moisture conditions; the sum dynamics of the first three enzyme species across all the isozyme families (= the sum Variance Contribution Ratio (VCR) of the first three enzyme species in matrix S), represents the variation of the total zymograms over the whole simulated moisture conditions.

Hypotheses:
1.The higher variation in biochemical dynamics of enzyme expression, the better environmental adaptiveness or immunology (the reason of this hypothesis is presented in chapter 7 of this book). It is deduced that the biochemistry dynamics of the first three isozyme families, which show the highest variation by PCA, determines the conclusion of this comparison;

2.Sample 2 leads to higher variation in biochemical dynamics of enzyme expression, which is also revealed by the higher adaptiveness during drought stress or higher immunology.

Discussion:

The findings of this chapter further support the theory, ‘memory’ of gene expression, proposed by other articles of this journal. This means that the population does not only pass on the genome, the genetic resource, but also passes on the ‘memory,’ in terms of identifying the bio-signal triggering the gene expression, onto their offspring. If these two kinds of bacteria cultivation methods lead to different gene expression types, then the second bacteria cultivation method is closer to the field conditions. Definition of bio-signal in this book as environmental physiology: the signals, emitted from environmental factors (both biotic and abiotic), can be perceived or identified by living beings; However, the memory of cells can be ‘trained’ by the biophysical simulation in site, indicated by the zymograms in metabolomics test. Consequently, the memory of cells, in terms of identifying the bio-signals of an environmental factor (can be biotic or abiotic) triggering the gene expression for environmental adaptiveness or immunology, can be trained by the biophysical simulation of other environmental factors. The appendix of this chapter (biophysical simulation for blood cell division) further supports above theories (please note: the theory, ‘memory’ of gene expression, is also applicable on cell division in an individual) by assessment of resistance or immunology in host cells.









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. Firstly Revised on 05/01/2021; Secondly Revised on
06/02/2021.

References:
[1] 陶玲,任裙 (2004)。进化生态学的数量研究方法。第一章,第六节,第 49 页。 中国林业出版社。 ISBN:7-5038-3735-7.
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