Essay: original review of specificity in the interaction between pathogen inv...

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Essay: original review of specificity in the interaction between pathogen invasion and host organism

Author: Liu Huan (1983- ), Master of Science (First Class Honours), The University of Auckland.

Key points of this article:

There are three main parts with regards to the topic ‘specificity in the interaction between pathogen invasion and host organism’: firstly, the specificity in population genetics between invasive pathogen genotype and host genotype (including specific host cells, tissue, organ or individual); secondly, the specificity in metabolic biochemistry pathways between invasive pathogen phenotype and host phenotype, which is further discussed below; third, the specificity in cultural or ecological conditions (such as specific season, geography site, pathogen transmission pathways [4]) between pathogen invasion and host organism.

A novel matrix of Matrix Xsum is designed for the classification across different bio-samples of host cells [1]. However, This classification methods is also applicable on the identification of virus phenotype in the invasion-host experiment designed in my another article [2], and a combination of both genotype and phenotype classification method has been designed in my bacterial article previously [3]. Both virus and bacterial classification would help to improve the accuracy in the identification of pathogen strains. This is especially for epidemic pathogens with broad infection rate (such as COVID 19), because if there is only one indicator (such as genotype) to analyze, the specificity in the interaction between pathogen invasion and host organism may not be apparent, but the specific virus strain would be much more accurately identified once there are comprehensive indicators selected to analyze below, targeting specific host population.

Based on the specificity in the interaction between pathogen invasion and host organism, this article designs a new table covering the systematic indicators to identify and classify the pathogen strains.  

Table 1. The systematic indicators identifying and classifying the pathogen strains.

	Pathogen genotype	Pathogen phenotype	Host cell genotypes infected	Host cell phenotypes infected	Host cell genotypes and phenotypes with apparent immunology	Season to break out	Geography distribution (Is it origin?)	Pathogen transmission pathways
Pathogen Strain 1
Pathogen Strain 2
.......

As summarized in these articles [5][6][7][8], the majority of research with regards to the interactions between pathogen genotype and host genotype are from plant pathology studies, whereas pathological studies of mammals have seldom chosen this methodology to analyze, although limited studies have screened specific gene sequences on goat species infected by Paratuberculosis [19], which should become the research gaps to fill in. However, even for the plant pathology studies, they either emphasized on the pathogen genotype only such as [5][6] or focused on the host genotype only such as [7][8], without further discussing the interactions between both of them, which may become the shortage to exactly target the disease control methods. It is further noted that specific gene sequences that plays the key role in pathogen invasion physiology have been screened in the study [5][6]. In comparison, various gene mutation types of COVID-19 virus have been summarized by Banda et al.,(2023), followed by the public emotional responses on Twitter social media [15]. However, among these gene mutation sequences, much fewer studies have conducted the specificity research pointing out which specific gene sequence expressed as the invasive physiology like studies [5][6], as my another article argues that ‘only a small proportion of occurrences in gene mutation may be directly related to the characteristics of virus invasive biology against host cells, which consequently should not overstate Big,[16]’ avoiding unnecessary public nervous or panic emotions during pandemic period.  

As discussed in these papers [9][10][11][12][13], a number of non-specific  immunological enzyme families, mainly including acid phosphatase, alkaline phosphatase, total antioxidant capacity, superoxide dismutase, catalase and malondialdehyde, have been selected as indicators to analyze the effects of baits, high temperature, PH threat, low salts and marine red yeast on the physiology of aquatic species respectively. In these studies, the chosen enzyme species were classified into non-specific ones. However, as designed in my another metabolomics article [14], specific enzyme species may be identified at exact molecular weight level within an isozyme family which contains one of the above functional groups of immunological enzyme, which may become the improved methods to analyze the environmental effects on the aquatic physiology. The above functional groups of immunological enzyme becomes the indicator to synthesize the new isozyme primers used in isozyme electrophoresis experiment.

Without adopting Clone Technology, my environmental study tries to design a more natural method to screen the gene traits for functional biology study by summarizing above case studies, taking epidemiology disease as an example below:

Step 1. Bio-samples of both host cells and pathogens are cultivated separately in Lab, and then simulation of pathogen invasion against host cells is conducted under Lab conditions. Then different phenotypes of both pathogen and host cells are identified and classified.

Step 2. To screen and identify the specific isozyme families involved in the invasion-immunology interactions through isozyme electrophoresis experiment, by comparing each phenotype of pathogen or host cell with the corresponding background bio-samples that are cultivated without implementing the simulation of pathogen invasion against host cells. The specific enzyme species within an isozyme family can be identified at exact molecular weight level, and the corresponding bio-materials of enzyme species identified in electrophoresis pipes can be collected for further analysis (such as to further characterize the structure of enzyme molecule by structural biology study for bio-medicine production);

Step 3. According to the functional groups of isozyme family screened in above experiment, preliminary screening of gene sequences can be implemented in Gene Bank by using bio-informatics technology, aiming to the design of primers for  Polymerase Chain Reaction (PCR) experiment; After PCR experiment testing each phenotype and background bio-sample, the polymorphism gene loci are screened by comparing different electrophoresis bands among various phenotypes and background sample.

Step 4. The gene materials identified in the electrophoresis bands can be collected for the purpose of further gene sequencing experiment, leading to the specific gene sequences identified in the polymorphism gene loci;

Step 5. The correlation between the specific gene sequences identified and the gene expression as the specific enzyme species are analyzed by comparison across different phenotype bio-samples and the background ones in the interaction between pathogen invasion and host defence.

Step 6. Gene Silencing technology is selected to further identify the gene traits of specific gene sequences screened in above experiment, which have been applied over a broad range of biological kingdom, including plants, nematodes, fungi, insects, protozoa and mice [18].   

Step 7. After the specific gene sequences with specific expression function is identified, the corresponding gene sequences can be used to design the DNA probes in FISH technology, which is applicable on the gene mapping technology. Then this specific gene sequences can be mapped on the specific genome.     

In summary above, the full specificity research in the interaction between pathogen invasion and host organism should identify the specific gene sequences expressed as specific enzyme species at molecular weight level in the invasion - immunology physiology process, under the regulator of specific abiotic environmental conditions. This is the one of the principal natural Laws underlying evolutionary process in natural ecosystem.  

The advantages of the new experiment methods designed above: firstly, the gene traits are screened by natural methods, other than the anti-nature method of Clone Technology, so that all the molecular biological functions are studied under the natural Law by evolutionary genetic analysis. My environmental study insists The Principle of Nature: only when the genetic resource is natural evolved, the creatures can pass on it into their offspring through the reproduction process; Secondly, this experiment starts the screening process by screening the specific isozyme families involved in the functional process at first, which should become more efficient and save time, because the total information of functional groups in isozyme families is much more limited than the DNA sequences database and the specific enzyme species playing the key role in the functional process can be easily identified and separated in the electrophoresis pipes for further analysis; If other biological functions (such as drought tolerance, reproduction traits or other genetic diseases) are chosen for study, the phenotype identification process in step 1 of above experiment method would be replaced accordingly, which requires to screen different isozyme families correspondingly.  

An original review essay is coming as the first study plan in this year (not less than 10 000 words in English)......

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[3]. Liu Huan. (2021). Classification of Bacteria by DNA Genetic Marker and Its Theory. Journal of Environment and Health Science (ISSN 2314-1628), 2021(02).

[4].Liu Huan (2022). Epidemiology------Comparison between indoor and outdoor air quality at three representative sites in Auckland Center. Journal of Environment and Health Science (ISSN 2314-1628), 2022(12).

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Firstly published at 05:30PM 13/01/2023. Secondly revised at 11:30PM 13/01/2023. Third revised on 14/01/2023. Fourthly revised on 29/01/2023. Fifthly revised on 20/02/2023a. Sixth revised on 20/02/2023b. Seventh revised on 21/02/2023. Eighthly revised on 24/02/2023 a;b. Ninthly revised on 26/02/2023. Tenthly revised on 27/02/2023 a;b.