Lab Assessment of E. Coli Sakai Growth in Spinach Leaf Lysate Solution

Introduction
The discovery of E. Coli by Theodor Escherichia in 1885 led to a breakthrough in the
field of science. Being a facultative anaerobe, certain serotypes of E.coli are harmless. Its
virulence factors include production of Shiga toxins, intestinal colonization and possessing
putative virulence plasmid referred to as pO157. E.coliO157:H7 causes food borne illness,
having severe symptoms on humans, (McGann, 2016 pp 4420). Prevalence of food borne
illness are estimated to have a mortality rate of 60 deaths per year, 2300 hospitalization rate
and 73,000 incidence rate as per the year in USA, (Hasman etal, 2016).
E. coli can be transmitted though contamination of water and soils. Further its
transmission can take place through plants and animals through the usage of flagella into the
cell walls of plants, (Sharapov et al, 2016 pp 2025).
E. coli presences have been found in plant surface and contaminate fresh vegetables
such as spinach, lettuce and sprout seed. The resistance has been noticed even after washing
the vegetable making it hazardous. Further bit can penetrate through plant cells through the
root system and contaminate food plants thus causing diseases. In plants such as the lettuce,
there surfaces can harbor E. coli which is resisting on the surface of the surface even after
washing, it is spread to the stomata and on the leaves. Further they can penetrate through their
root systems which eventually get onto the sizable parts. Further soils, water and animals can
contribute to or lead to contamination in the farm.. Thus the strain can be found on the fruits
parts of the plants. Further the strain has been observed t enter through leaf structure of
plants, causing disinfection of plants, (Schmidt et al, 2016).
Laboratory assessment of E.Coli
Lab assessment of E coli has been ongoing in the Holden lab of James Hutton
University taking the lead. The culture of E coli Sakai was made in minimal media refer to as
LB broth and shown splitting process into various minimal media culture which has a leaf
lysate. After full growing of the E coli, in the spinach leafy state with the minimal media,
RNA sequence was performed in 3 parts and the readings taken to understand the various
interactions which have been initiated on the interaction between bacteria and plant host in
order to minimize the risks of acquiring food borne illness.
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Lab results and analysis
Data analysis
In assessing this experiment, principal component analysis was performed, where
maximum variables of samples were done. This ensured visualization of the samples
relationships. Principle component analysis allows for transformations of PC 1 in horizontal
axis while the PC 2 on the vertical axis. This data indicated PC1 variation o the right side
with 86.03% while PC2 had 6.81%.
Cluster analysis
On performances of cluster analysis, the two culture media were separated into leafy
lysate and minimal media. This illustration indicated more closely related values. This
signifies that the individual; replicates exhibit almost no formal structure. The graphs of the
leaf lysate and minimal media are closely separated. This indicates that the replication is
almost similar. The p-values indicating of approximate unbiased value, which is reflective of
bootstrap value which has overall measurement of the branching pattern.
Scatter plot analysis
Scatter plot analysis using the FDA seq package using principle component analysis
and clustering was done. Using Edge R, the estimate of the variation was assessed, with high
biological value affecting the ability to identify the expressed genes. Further the use of edger
was used in identification of differential expression of genes. Top genes were significantly
expressed. Edge R is effective on identification of differential expression. Each of the 10
genes has been expressed as shown by the P-values. Each has a special description of the
specific gene. Evaluation of large scale differential expression having three biological values
provides clerical fold change. For many cases, log count per million signifies fold change
which is appropriate and reliable. These results illustrate the fold change being 2, which has
high relativity value. Fold change is often high or low. As log changes, and then there is
biological significant difference which exist. Thus as the read count is high so do the log fold
change, which confirms the significance of the genes, (Wallden et al, 2016). Dispersion
reflects the dispersion of data over time; the genes are trended having similar expression as
those of dispersions in the gene direction. Display tag wise dispersion often indicates the
common value. This justifies the use of log changes which predicts significant difference in
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the gene expression.
Volcano plot an functional annotation analysis
When the two media are assessed on a volcano, there exhibit high points of positive and
negative values, while those at the lower bottom have nice folder change however indicating
false discovery rate, thus indicating low significance. Expressions of the significant genes on
mapping showed 41% of the presence. Green gene halos showed down regulation while the
red halo genes were up regulated while genes with halo yhcN and bright green gen expressed
could have significance based on its high level expression, (Liu et al, 2016). Thus the reliance
of fold change can be high or low, thus justifying the need for log field changes which have
high representation through biological significance in terms of expressions. Hence the
investigation of biological differences as indicated in the read count can be high while the log
change further signifies high values, thus confirming high significant biological genes.
KEGG pathways visualization
Expression on KEGG pathway revealed important functions on the metabolic pathway.
Presence of ion sensor and nutrient transporters found on the leafy state, further sulfur and
carbon metabolism enzymes were over expressed.
The pathway of copper on the KEGG pathway shows that there is a display on ABC
transporters. Copper is under expressed in the pathway, while there is an up regulation of the
ion sensors on the nutrient transporters in the leafy state. The association of the up regulation
ion sensors and nutrient linkages in the leaf lysate have shown to be illustrative of gene
expression. On the other end sulfur and carbon metabolisms enzymes shows over expression.
Thus sulfur and carbon have been shown to have enzymes which are metabolically over
expressed.
Discussion
E coli strains have been shown to utilize plants being host and becoming internalized
causing interaction with the plant o a molecular level. Based on this investigation on the
responses of E coli O157:H7 Sakai growth in spinach leaf lysate solution was compared with
the minimal media, (Rasmussen & Bell, 2017). Its performance was made using RNA seq
with different expression analysis for determination of genes which are essential for the
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