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  • Metabolomics Practical Assignment.Wet Lab. Question 1.Both water and methanol are used to allow a simultaneous extraction of both polar and apolar compounds. Methanol extracts the apolar compounds whereas water, on the other hand, extracts the polar compounds from the plant specimen. The use of methanol and water during extraction results in a biphasic separation, where the aqueous phase is freed from the phospholipids and lipids to allow its separate analysis (Inamuddin, , and Ali, 13-17).Question 2.Internal standards help calibrate the system. They are applied for the quantitative analysis precision improvement by behaving like the analyte and provide distinctive signals. In the chromatographic phase of the extraction, the internal standards provide correction for the variability caused by the loss of analyte in sample treatment and storage.Question Derivatization of 3.compounds allows their chemical change to produce new chemicals that are better suited for the GC-MS analytical process. Compounds with poor thermal stability, poor volatility or that can be adsorbed in the injector tend to express nano-reproducible heights, shapes and peak areas. Besides, compounds with poor response to the specific detection method can be tagged with the specific functional group for detection improvement (Inamuddin, , and Ali, 67-69). Derivatization is also used as a method of improving resolution between overlapping peaks and coeluting compounds.Question 4.The isocratic elution consists of a constant mobile phase throughout the separation process, but the gradient elution consists of varying mobile phase along the run. The isocratic mode is suited for the separation of two or three compounds in just one run (Inamuddin, and Ali, 68-73). On the other hand, the gradient mode is most suited for the separation of substances of different polarity and whose separation cannot be achieved in one mobile phase.Question Beta-carotene is an (a) 5.apolar substance. Its basic structure composes iso-propene, and it contains three bonds, namely C-C, C=C and C-H, which are responsible for its apolar hydrocarbon property. The compound dissolves easily in non-polar solvents like chloroform, benzene and carbon disulfide but practically insoluble in alkalis, acids and water (b).The best type of solvent applicable in the extraction of beta-carotene is the non-polar solvents. The best examples of the applicable solvents are chloroform and benzene. Beta-carotene is non-polar, and it cannot dissolve in the polar solvents like water, alkali and acids hence the use of non-polar substances like the chloroform and Bioinformatics. benzene (Inamuddin, and Ali, 19-23).Question 1.Log transformation is performed prior to the statistical analysis of the metabolomics data to serve two major purposes. One of the reasons for log transformation is the more reduction of large values in relation to the small values. Additionally, log transformation serves the purpose of removing heteroscedasticity (Semmar, 32-48).Question 2.If the p-value threshold changes to 0.1 from 0.05, there is an increased certainty of proving the null hypothesis true but if the change is from 0.2 to 0.1, the certainty of proving the null hypothesis true reduces. The reason for this observation is because of the increase of the confidence interval that is caused by the increase of the p-value in the t-test.Question 3.The principal component analysis allows the representation of data in spatial dimensions of columns and variables as well as help look for patterns. The plot produces a 3D view of the data. A recommendation to this technique comprises the linear discriminant analysis which has a class separability optimization (Semmar, 24).Question 4.When performing multiple significant tests, it is important to correct for false positives to avoid the introduction of the type two error that could cause erroneous conclusions. Type 2 error introduction happens when a single data set is subjected to numerous pair wise tests, leading to the possibility of the identification of more than one significant test (Semmar, 27 and 28).Question Aspartate 5.and alanine metabolism (Homo sapiens).The top five enriched pathways at the threshold 0.05 are reductive carboxylate cycle, lysine biosynthesis, histidine metabolism nicotinamide metabolism and fatty acid metabolism. The top five enriched (KEGG) pathways at the threshold p=0.1 are glycolysis and gluconeogenesis, reductive carboxylate cycle, urea cycle, lysine biosynthesis and b-alanine metabolism. The change observed, in this case, results from the difference in p-value size application during t-testing.

Metabolomics Practical Assignment.Wet Lab. Question 1.Both water and methanol are used to allow a simultaneous extraction of both polar and apolar compounds. Methanol extracts the apolar compounds whereas water, on the other hand, extracts the polar compounds from the plant specimen. The use of methanol and water during extraction results in a biphasic separation, where the aqueous phase is freed from the phospholipids and lipids to allow its separate analysis (Inamuddin, , and Ali, 13-17).Question 2.Internal standards help calibrate the system. They are applied for the quantitative analysis precision improvement by behaving like the analyte and provide distinctive signals. In the chromatographic phase of the extraction, the internal standards provide correction for the variability caused by the loss of analyte in sample treatment and storage.Question Derivatization of 3.compounds allows their chemical change to produce new chemicals that are better suited for the GC-MS analytical process. Compounds with poor thermal stability, poor volatility or that can be adsorbed in the injector tend to express nano-reproducible heights, shapes and peak areas. Besides, compounds with poor response to the specific detection method can be tagged with the specific functional group for detection improvement (Inamuddin, , and Ali, 67-69). Derivatization is also used as a method of improving resolution between overlapping peaks and coeluting compounds.Question 4.The isocratic elution consists of a constant mobile phase throughout the separation process, but the gradient elution consists of varying mobile phase along the run. The isocratic mode is suited for the separation of two or three compounds in just one run (Inamuddin, and Ali, 68-73). On the other hand, the gradient mode is most suited for the separation of substances of different polarity and whose separation cannot be achieved in one mobile phase.Question Beta-carotene is an (a) 5.apolar substance. Its basic structure composes iso-propene, and it contains three bonds, namely C-C, C=C and C-H, which are responsible for its apolar hydrocarbon property. The compound dissolves easily in non-polar solvents like chloroform, benzene and carbon disulfide but practically insoluble in alkalis, acids and water (b).The best type of solvent applicable in the extraction of beta-carotene is the non-polar solvents. The best examples of the applicable solvents are chloroform and benzene. Beta-carotene is non-polar, and it cannot dissolve in the polar solvents like water, alkali and acids hence the use of non-polar substances like the chloroform and Bioinformatics. benzene (Inamuddin, and Ali, 19-23).Question 1.Log transformation is performed prior to the statistical analysis of the metabolomics data to serve two major purposes. One of the reasons for log transformation is the more reduction of large values in relation to the small values. Additionally, log transformation serves the purpose of removing heteroscedasticity (Semmar, 32-48).Question 2.If the p-value threshold changes to 0.1 from 0.05, there is an increased certainty of proving the null hypothesis true but if the change is from 0.2 to 0.1, the certainty of proving the null hypothesis true reduces. The reason for this observation is because of the increase of the confidence interval that is caused by the increase of the p-value in the t-test.Question 3.The principal component analysis allows the representation of data in spatial dimensions of columns and variables as well as help look for patterns. The plot produces a 3D view of the data. A recommendation to this technique comprises the linear discriminant analysis which has a class separability optimization (Semmar, 24).Question 4.When performing multiple significant tests, it is important to correct for false positives to avoid the introduction of the type two error that could cause erroneous conclusions. Type 2 error introduction happens when a single data set is subjected to numerous pair wise tests, leading to the possibility of the identification of more than one significant test (Semmar, 27 and 28).Question Aspartate 5.and alanine metabolism (Homo sapiens).The top five enriched pathways at the threshold 0.05 are reductive carboxylate cycle, lysine biosynthesis, histidine metabolism nicotinamide metabolism and fatty acid metabolism. The top five enriched (KEGG) pathways at the threshold p=0.1 are glycolysis and gluconeogenesis, reductive carboxylate cycle, urea cycle, lysine biosynthesis and b-alanine metabolism. The change observed, in this case, results from the difference in p-value size application during t-testing. Essay

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Metabolomics Practical Assignment.Wet
Lab. Question
1.Both
water
and methanol are used to allow a simultaneous
extraction of both
polar
and apolar compounds. Methanol extracts
the apolar compounds
whereas
water, on the
other
hand, extracts
the
polar
compounds from the
plant
specimen. The
use of methanol and
water during extraction
results in a biphasic separation, where
the aqueous phase is freed from the phospholipids and lipids to allow its separate analysis
(Inamuddin, , and Ali, 13-17).Question
2.Internal
standards
help calibrate the
system. They
are applied
for
the quantitative analysis
precision
improvement by behaving like the analyte and
provide
distinctive
signals. In the chromatographic phase of the
extraction, the
internal
standards
provide
correction
for
the variability caused by the
loss of analyte in sample
treatment
and
storage
.Question Derivatization of
3.compounds
allows their chemical
change to produce
new
chemicals that are better
suited
for
the GC-MS analytical
process. Compounds with poor
thermal
stability, poor
volatility
or that can be adsorbed in the injector tend to express nano-reproducible heights, shapes
and
peak
areas. Besides, compounds with poor
response to the
specific
detection
method can be tagged with the
specific
functional
group
for
detection
improvement (Inamuddin, , and Ali, 67-69). Derivatization is also
used as a method of improving
resolution between overlapping
peaks
and coeluting compounds
.Question
4.The isocratic elution consists of a constant
mobile
phase throughout the
separation
process, but
the gradient elution consists of varying
mobile
phase along the
run. The isocratic mode
is suited
for
the
separation of two or three compounds in just one run (Inamuddin, and Ali, 68-73). On the
other
hand, the gradient mode is most
suited
for
the
separation of substances of different
polarity
and
whose
separation cannot be achieved in one mobile
phase
.Question Beta-carotene is an
(a)
5.apolar
substance. Its basic
structure
composes iso-propene, and
it
contains three bonds, namely C-C, C=C and C-H, which are responsible
for its apolar hydrocarbon property. The
compound
dissolves
easily in non-polar solvents like chloroform, benzene and
carbon disulfide but
practically
insoluble in alkalis, acids
and
water
(b)
.The
best
type of solvent applicable in the
extraction of beta-carotene is the non-polar solvents. The
best
examples of the
applicable
solvents are chloroform and benzene. Beta-carotene is non-polar, and
it cannot dissolve in the
polar
solvents like water, alkali
and
acids
hence
the
use of non-polar substances like the chloroform and
Bioinformatics.
benzene (Inamuddin, and Ali, 19-23).Question
1.Log
transformation is performed
prior to the
statistical
analysis of the metabolomics data to serve two major
purposes. One of the
reasons
for
log
transformation is the
more
reduction of large
values
in relation to
the
small
values. Additionally, log
transformation
serves
the
purpose of removing
heteroscedasticity (Semmar, 32-48).Question
2.If
the p-value threshold
changes to 0.1 from 0.05, there is an increased
certainty of proving
the
null
hypothesis
true
but
if
the
change is from 0.2 to 0.1, the
certainty of proving
the
null
hypothesis
true
reduces.
The
reason
for
this
observation is because of the
increase of the
confidence
interval that is caused by the
increase of the p-value in the
t-test.Question
3.The
principal
component
analysis
allows
the
representation of data in spatial dimensions of columns
and variables as well as help
look
for
patterns. The
plot
produces a 3D view of the data. A
recommendation to this
technique
comprises
the
linear discriminant analysis
which has a class
separability optimization (Semmar, 24).Question
4.When
performing
multiple
significant
tests, it is important to correct
for
false positives to avoid
the
introduction of the
type two error that could cause
erroneous
conclusions. Type 2 error
introduction
happens
when a single
data
set is subjected to numerous
pair
wise
tests, leading to the
possibility of the
identification of more than one significant
test (
Semmar, 27 and 28).Question Aspartate

5.and

alanine metabolism (Homo sapiens).The
top five enriched pathways at the
threshold 0.05 are reductive carboxylate cycle, lysine biosynthesis, histidine metabolism nicotinamide metabolism and
fatty
acid metabolism. The
top five enriched (KEGG) pathways at the
threshold p=0.1 are glycolysis and gluconeogenesis, reductive carboxylate cycle, urea cycle, lysine biosynthesis and b-alanine metabolism. The
change
observed, in this
case, results from the
difference in p-value size
application during t-testing.

Work cited.

Inamuddin, , and Ali Mohammad. Green Chromatographic Techniques: Separation and Purification of Organic and Inorganic Analytes. , 2014. Internet resource.

Semmar, Nabil. Computational Metabolomics. New York: Nova Science Publishers, 2011. Internet resource.