Rapid Methods in Food Analysis Practical Manual - Students

Rapid Methods in Food Analysis– A Practical Manual
DEPARTMENT OF FOOD SCIENCE

FACULTY OF FOOD SCIENCE AND TECHNOLOGY
RAPID METHODS IN FOOD ANALYSIS

(FST4201)
A PRACTICAL MANUAL
1 FST4201 | Faculty of Food Science and Technology, UPM

TABLE OF CONTENTS
No. Topic Page
1. Introduction
§ General Laboratory Safety Instruction 3
§ Guidelines for Report Preparation and Submission 6
§ Practical Skills Evaluation Assessment Criteria 9
§ Writing Lab Reports and Scientific Papers 11
2. Practical 1: Isolation of Vibrio parahaemolyticus using one-step and 16
two-step enrichment methods
3. Practical 2: Isolation of Listeria monocytogenes using one-step 20
enrichment method
4. Practical 3: Isolation of Escherichia coli O157:H7 using one-step and 24
two-step enrichment methods
5. Practical 4: Extraction of DNA from human cheek cells by spooling 28
6. Practical 5: Extraction of genomic DNA from bacteria 32
7. Practical 6: Identification of pathogen using polymerase chain reaction 37
(PCR)
Practical 7: Visualisation of PCR amplicons by gel electrophoresis 44
Practical 8: Designing oligonucleotides (primers) for PCR 48
Practical 9: Diagnostic method for the detection of food allergens – 52
quantitative determination of total soluble proteins using Bradford
assay.
Practical 10: Detection of allergens in food samples using enzyme- 62
linked immunosorbent assay (ELISA)
Practical 11: Rapid detection of mycotoxins from food samples using 73
immune biosensor (demonstration)

General Laboratory Safety Instruction
Learning Objectives:
At the end of this laboratory session, students should be able to:
1. Understand the laboratory safety rules

2. Comply and apply the Good Laboratory Practice throughout the laboratory sessions
Good Laboratory Practice includes the following:

Be aware/Take care • Be familiar with all lab operations, procedures and
equipment
• Injuries may arise from careless treatment, common
operations.
• Always endeavor to be aware of the possible implications
of every action/inaction
• Work with another person present (if possible)
• Caution when handling needles and syringes
Hazardous Materials • Learn about the hazardous properties of all materials
used in the workplace.
• Observe safe handling, storage, disposal and emergency
procedures. Treat unknown materials as potentially
hazardous
Knowledge of Be knowledgeable about:
emergency • Emergency reporting procedures, telephone numbers,
procedures/Location of location of telephones
emergency equipment • Floor lay-out, location of exists and designated
evacuation routes, exit procedures, sound of fire alarm,
location of fire alarm pull stations and fire extinguishers
• Operating procedures for all safety and emergency
equipment
Personal Protective • Wear appropriate PPE (e.g. laboratory coats or gowns,

Equipment (PPE) gloves, safety goggles or face shields, aprons) for the
work being conducted
• Wear closed shoes, with heels not more than 1 1/4 “ in
height
• Secure scarf/hair/beard if its length may interfere with
laboratory work
• Restrain loose clothing. Remove jewelry when working
with chemicals, biohazards, radioactive material, flames
or moving machinery
• Pack your lab coats in a separate bag
Ingestion of hazardous • Do not eat, drink or smoke in the laboratory; apply lip
materials salve; cosmetics or contact lenses, insert fingers, pencils,
etc. in the mouth, lick envelopes or labels
• Do not store food or beverages in any refrigerator that
contains body substances or chemicals. Label all
refrigerators and freezers that contain body substances
as biohazardous.
• No food and beverages in the lab
Work Area • Keep work area neat, organized and free of clutter
• Clean and decontaminate work surfaces at the end of
each class
• Keep lab corridors free of obstructions and tripping
hazard
• Do not use decorations that can be contaminated or
present a fire hazard
• Keep personal property out of the laboratory area
Chemicals • Conduct procedures using volatile, toxic or flammable
chemicals in a chemical fume hood
Biosafety • Sterilize all instruments/items that were in contact any
body fluids, microbial matter or any potentially infectious
agent
• Place all culture and contaminated materials in the
appropriate disposal area for sterilization

• Place microscope glass slide in disinfectant

• Use disinfectant soap to wash hands after work
Biohazardous aerosol • Conduct procedures potentially generating aerosols in a
biological safety cabinet
Airborne contamination Reduce airborne contamination by:
• Avoiding strong movements of air while handling culture
(Eg. Coughing, sneezing)
• Avoiding from dropping contaminated pipettes or tips
onto a hard surface
• Being careful with inoculating loops during work
Pipetting • Use only mechanical pipetting devices for pipetting. Do
not mouth pipette
Access • Only authorized personnel have access to the laboratory
• Do not have friends visit you in the laboratory
Equipment • Check the safe working condition of all equipment before
operating it
Spills • Report all spills to the instructor/demonstrator/lab officer
Accidents • Report ALL accidents, incidents and adverse health
effects related to working in the laboratory immediately.

Guidelines for Report Preparation and Submission
1. The cover page of the report should contain the following information:
a. Experiment number and title
b. Group No.
c. Group member who attended the laboratory practical (the name of any member who did
not attend the laboratory session need not be included. You may choose to omit the name
of a member who did not contribute in the preparation of the report)
d. Date of laboratory practical
2. Each report should contain the following:

a. Abstract (summary of the objective, method and results obtained. Do not include
discussion and references)
b. Introduction including the objective of experiment
c. Materials and Methods (especially if modifications in procedure have been made)
d. Results and Discussion. Do not include calculations and refer to food composition tables
whenever possible to compare the results you had obtained. Provide reasons that might
have caused differences in values eg. Different variety of sample used etc. (Tables must
have title above, while figures and graphs must have title below)
e. Conclusion
f. Answers to questions provided in the laboratory manual, or by the coordinators
g. References must be cited in the text and listed in the Reference at the end of the report
(Use the style of the Journal of Food Science in your reference list and in citations in the
text available at http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1750-3841).
h. Appendices (all raw data and experimental calculations must be included)
3. A data should be presented in one form only. If you choose to tabulate your data, do not
present the data again in the form of a graph, and vice versa. A graph may be plotted using
any suitable software.
4. Report must be submitted to the course coordinator two weeks after the laboratory practical
has been conducted.
5. Each group submits one report only.
6. Plagiarism: Plagiarism in practical reports will not be tolerated. A ZERO mark will result for
any report found to be plagiarised from another student’s report. This other student’s report
will also be given a zero mark. Plagiarism particularly applies to copying whole sections of text
from another person’s report. You are encouraged to collaborate on data analysis, particularly
on the required calculations, but the written report must be your own work.

Laboratory Report Assessments Rubric
Report Elements Very Poor (1) Poor (2) Moderate (3) Good (4) Very Good (5) Weightage
Duplication of Missing the major

Missing some part Complete and A well-written
introduction and finding. Lack of
of the major finding accurate abstract abstract that is
Abstract results. Not understanding on 1
but follow a proper with minor complete and
following the given writing a proper
abstract format. mistakes accurate.
guidelines. abstract.
Incomplete
Nearly complete
Very little information
introduction with Substantial A complete and a
background provided and major
relevant points introduction with well-written
information points are not
provided. Missing relevant points introduction.
provided. properly
some minor point. provided.
Introduction and addressed.
2
Objectives
Clearly stated
Irrelevant Satisfactorily Well-stated objective, highly
objectives. Satisfactorily
formulated objective, relevant relevant to the
formulated
objective relevant to the topic. topic
objective relevant
to the topic
to the topic
Missing most of
Missing some of
the important Well-written and
the important Complete but not Complete and
Materials and experimental all experimental
experimental accurate with accurate with 1
Methods details and not details are
details. Written in some mistakes. minor mistakes.
written in covered.
paragraph format
paragraph format.

Capable of
Capable of
producing results
producing results
Capable of Capable of which is better
with good
producing results producing results than the
accuracy.
Unable to produce but with low with acceptable expectation.
Graphical are
good results. accuracy. Some accuracy. Minor Graphical are
correctly drawn.
Graphical are Graphical are poorly graphical errors. correctly drawn.
Results and
poorly constructed. constructed. 3
Discussion Almost all results
Some results have All results have
have been
Little/no discussion Inadequate/incorrect been correctly been correctly
correctly
on the results. discussion. Limited interpreted with interpreted and
interpreted with
understanding of moderate discussed. Good
good
results. understanding. understanding of
understanding of
results is carried.
results.
Missing or not States some findings The main findings State the main Very well
satisfactorily but not all. Many are have been drawn, findings and their formulated. All-
related to results or misstated indicating could be better implications in a important
not relevant to a lack of stated. short- and long- conclusions have
Conclusion 1
objective understanding. term perspective. been clearly
made, student
shows good
understanding
Unable to answer Able to answer Able to answer Able to answer Able to answer
Ability to Answer all questions. basic question most questions, most questions all questions with
1
Questions without proper but fails to with proper suitable
explanation. elaborate. explanations. explanations.
Poorly organized
Disorganized Organized report Neat and easy to Well-organized
report with
report with a lot of with some read report with report with no
Report Quality occasional 2
grammar/spelling grammar/spelling minor grammar/ grammar/spelling
grammar/spelling
errors. errors. spelling errors. errors
errors.

Practical skills evaluation assessment criteria
Up to maximum of 1-5 % per indicator (to be evaluated in each practical session):
1. attendance at all laboratory sessions;

2. amount of effort put into laboratory practical exercises;
3. amount of preparation undertaken prior to entering the laboratory;
4. quality of performance in the laboratory;
5. confidence in the laboratory;
6. student-student interaction in the laboratory;
7. student-staff interaction in the laboratory.

Psychomotor Assessments Rubric

Sub- Very Poor Poor Moderate Good Very Good Score and
Attribute
Attributes (1) (2) (3) (4) (5) Comments
Capable of
Unable to Capable to use Master in the
identifying the Capable to use
identify and fail the related usage of related
proper the related
to use correct instruments but instrument
Work training instruments. instruments with
instruments lacking in skill throughout the
But, unable to confident.
Leadership and confident experiment.
use it properly.
Response
Capable of
Require Require Require Require
completing the
complete frequent moderate minimum
work task
Self-reliance guidance for the guidance for the guidance for the guidance for the
without further
work tasks. work tasks. work tasks. work tasks.
guidance.
Lack in Show some
Conscious
conscious and conscious but Conscious
No conscious about safety and
kurang obey kurang obey about safety and
Awareness of and unable to obey majority
majority of the majority of the obey all rules
hazards follow the safety of the rules
rules stated in rules stated in stated in the
guideline stated in the
the safety the safety safety guideline
Mechanism guideline guideline safety guideline
Capable of Capable of
Capable of Capable of
Unable to producing producing
producing producing
Productivity produce any results with results which is
results but with results with
results acceptable better than the
low accuracy. good accuracy.
accuracy. expectation.
Capable of
Capable of Capable of Capable of
Unable to completing
completing the completing the completing the
Complex complete the majority of the
Work delivery task but not up task according task which is
Response requirement of task but not up
to the to the better than the
the given task to the
standard. standard. standard.
standard.

Writing Lab Reports and Scientific Papers

by Warren D. Dolphin (Iowa State University)
Verbal communication is temporal and easily forgotten, but written reports exist for long periods and
yield long-term benefits for the author and others.
Scientific research is a group activity. Individual scientists perform experiments to test
hypotheses about biological phenomena. After experiments are completed and duplicated,
researchers attempt to persuade others to accept or reject their hypotheses by presenting the
data and their interpretations. The lab report or the scientific paper is the vehicle of persuasion;
when it is published, it is available to other scientists for review. If the results stand up to criticism,
they become part of the accepted body of scientific knowledge unless later disproved. In some
cases, a report may not be persuasive in nature but instead is an archival record for future
generations. For example, data on the distribution and frequency of rabid skunks in a certain year
may be of use to future epidemiologists in deciding whether the incidence of rabies is increasing.
Regardless of whether a report is persuasive or archival, the following guidelines apply.
Format
A scientific report usually consists of the following:
1. Title
2. Abstract
3. Introduction
4. Materials and methods
5. Results
6. Discussion
7. Literature cited
There is general agreement among scientists that each section of the report should contain
specific types of information.

Title
The title should be less than ten words and should reflect the factual content of the paper.
Scientific titles are not designed to catch the reader's fancy. A good title is straightforward and
uses keywords that researchers in a particular field will recognize.
Abstract
The purpose of an abstract is to allow the reader to judge whether it would serve his or her
purposes to read the entire report. A good abstract is a concise (100 to 200 words) summary of
the purpose of the report, the data presented, and the author's major conclusions.
Introduction
The introduction defines the subject of the report. It must outline the scientific purpose(s) or
objective(s) for the research performed and give the reader sufficient background to understand
the rest of the report. Care should be taken to limit the background to whatever is pertinent to the
experiment. A good introduction will answer several questions, including the following:
• Why was this study performed?
Answers to this question may be derived from observations of nature or from the literature.
• What knowledge already exists about this subject?
The answer to this question must review the literature, showing the historical development
of an idea and including the confirmations, conflicts, and gaps in existing knowledge.
• What is the specific purpose of the study?
The specific hypotheses and experimental design pertinent to investigating the topic should
be described.
Materials and Methods

As the name implies, the materials and methods used in the experiments should be reported in
this section. The difficulty in writing this section is to provide enough detail for the reader to
understand the experiment without overwhelming him or her. When procedures from a lab book
or another report are followed exactly, simply cite the work, noting that details can be found in
that particular source. However, it is still necessary to describe special pieces of equipment and
the general theory of the assays used. This can usually be done in a short paragraph, possibly
along with a drawing of the experimental apparatus. Generally, this section attempts to answer
the following questions:
What materials were used?

How were they used?

Where and when was the work done? (This question is most important in field studies.)
Results
The results section should summarize the data from the experiments without discussing their
implications. The data should be organized into tables, figures, graphs, photographs, and so on.
But data included in a table should not be duplicated in a figure or graph.
All figures and tables should have descriptive titles and should include a legend explaining any
symbols, abbreviations, or special methods used. Figures and tables should be numbered
separately and should be referred to in the text by number, for example:
1. Figure 1 shows that the activity decreased after five minutes.
2. The activity decreased after five minutes (fig. 1).
Figures and tables should be self-explanatory; that is, the reader should be able to understand
them without referring to the text. All columns and rows in tables and axes in figures should be
labeled. See appendix B for graphing instructions.
This section of your report should concentrate on general trends and differences and not on trivial
details. Many authors organize and write the results section before the rest of the report.
Discussion
This section should not just be a restatement of the results but should emphasize interpretation
of the data, relating them to existing theory and knowledge. Speculation is appropriate, if it is so
identified. Suggestions for the improvement of techniques or experimental design may also be
included here. In writing this section, you should explain the logic that allows you to accept or
reject your original hypotheses. You should also be able to suggest future experiments that might
clarify areas of doubt in your results.
Literature Cited
This section lists all articles or books cited in your report. It is not the same as a bibliography,
which simply lists references regardless of whether they were cited in the paper. The listing should
be alphabetized by the last names of the authors. Different journals require different formats for
citing literature. The format that includes the most information is given in the following examples:

For articles:
Fox, J.W. 1988. Nest-building behavior of the catbird, Dumetella carolinensis. Journal of
Ecology 47: 113-17.
For Books:
Bird, W.Z. 1990. Ecological aspects of fox reproduction. Berlin: Guttenberg Press.
For chapters in books:
Smith, C.J. 1989. Basal cell carcinomas. In Histological aspects of cancer, ed. C.D. Wilfred, pp.
278-91. Boston: Medical Press.
When citing references in the text, do not use footnotes; instead, refer to articles by the author's
name and the date the paper was published. For example:
1. Fox in 1988 investigated the hormones on the nest-building behavior of catbirds.
2. Hormones are known to influence the nest-building behavior of catbirds (Fox, 1988).
When citing papers that have two authors, both names must be listed. When three or more
authors are involved, the Latin et al. (et alia) meaning "and others" may be used. A paper by
Smith, Lynch, Merrill, and Beam published in 1989 would be cited in the text as:
Smith et al. (1989) have shown that...
This short form is for text use only. In the Literature Cited, all names would be listed, usually last
name preceding initials.
There are a number of style manuals that provide detailed directions for writing scientific papers.
Some are listed in further readings at the end of this section.
General Comments on Style

1. All scientific names (genus and species) must be italicized. (Underlining indicates italics
in a typed paper.)
2. Use the metric system of measurements. Abbreviations of units are used without a
following period.
3. Be aware that the word data is plural while datum is singular. This affects the choice of a
correct verb. The word species is used both as a singular and as a plural.
4. Numbers should be written as numerals when they are greater than ten or when they are
associated with measurements; for example, 6 mm or 2 g but two explanations of six
factors. When one list includes numbers over and under ten, all numbers in the list may
be expressed as numerals; for example, 17 sunfish, 13 bass, and 2 trout. Never start a
sentence with numerals. Spell all numbers beginning sentences.

5. Be sure to divide paragraphs correctly and to use starting and ending sentences that
indicate the purpose of the paragraph. A report or a section of a report should not be one
long paragraph.
6. Every sentence must have a subject and a verb.
7. Avoid using the first person, I or we, in writing. Keep your writing impersonal, in the third
person. Instead of saying, "We weighed the frogs and put them in a glass jar," write, "The
frogs were weighed and put in a glass jar."
8. Avoid the use of slang and the overuse of contractions.
9. Be consistent in the use of tense throughout a paragraph--do not switch between past and
present. It is best to use past tense.
10. 10. Be sure that pronouns refer to antecedents. For example, in the statement,
"Sometimes cecropia caterpillars are in cherry trees but they are hard to find," does "they"
refer to caterpillars or trees?
After writing a report, read it over, watching especially for lack of precision and for ambiguity. Each
sentence should present a clear message. The following examples illustrate lack of precision:
1. "The sample was incubated in mixture A minus B plus C." Does the mixture lack both B
and C or lack B and contain C?
2. The title "Protection against Carcinogenesis by Antioxidants" leaves the reader wondering
whether antioxidants protect from or cause cancer.
The only way to prevent such errors is to read and think about what you write. Learn to reread
and edit your work.
Readings
CBE Style Manual Committee. 1983. CBE style manual: A guide for authors, editors, and
publishers in the biological sciences. 5th ed. Bethesda, Md.: Council of Biology Editors.
McMillan, V.E. 1988. Writing papers in the biological sciences. New York: St. Martin's Press,
Inc.

Practical 1 : Isolation of Vibrio parahaemolyticus using one-step and two-

step enrichment methods
By the end of this experiment, students should be able to:
1. Isolate V. parahaemolyticus using standard enrichment method.
2. Understand the principles in each step in the enrichment method.
3. Understand the difference between using one-step and two-step enrichment methods.
Introduction:
Vibrio parahaemolyticus is known as a common foodborne pathogen in Asia, and has been
reported to be the cause for 20-30% food poisoning cases in Japan. It is a marine bacterium that
occurs naturally in coastal waters worldwide and is a cause of gastroenteritis with severe
abdominal pain and diarrhea. V. parahaemolyticus cases reported have most frequently been
attributed to the consumption of raw or undercooked seafood, or the ingestion of contaminated
water.
V. parahaemolyticus is a major food-borne pathogen that causes worldwide health problems.

Prevention of V. parahaemolyticus contamination of foods, which has been associated with recent
outbreaks, is an important public health concern. To establish effective control measures to
reduce the risk of V. parahaemolyticus infection and to ensure the safety of foods, efficient
analytical methods for the detection of V. parahaemolyticus in foods and the environment must
be available.
Selective enrichment with alkaline peptone water (APW) or salt polymyxin broth (SPB) and
plating of the enrichment culture onto thiosulfate citrate bile salts sucrose (TCBS) agar have
been widely used for selective isolation of V. parahaemolyticus from foods. TCBS agar is used
for the selective isolation of cholera vibrios and Vibrio parahaemolyticus from a variety of clinical
and non-clinical specimens. TCBS agar is highly selective for the isolation of V. cholera and V.
parahaemolyticus as well as other vibrios. Inhibition of gram-positive bacteria is achieved by the

incorporation of oxgall, which is a naturally occurring substance containing a mixture of bile salts,
and sodium cholate, a pure bile salt. Sodium thiosulfate serves as a sulfur source and, in
combination with ferric citrate, detects hydrogen sulfide production. Saccharose (sucrose) is
included as a fermentable carbohydrate for the metabolism of vibrios. The alkaline pH of the
medium enhances the recovery of V. cholerae. Thymol blue and bromthymol blue are included
as indicators of pH changes.
Typical colonial morphology on TCBS Agar is as follows:

V. cholerae ............................ Large yellow colonies.
V. parahaemolyticus ............. Colonies with blue to green centers.
V. alginolyticus ...................... Large yellow colonies.
Proteus/Enterococci ..............Partial inhibition. If growth, colonies are small and yellow to
translucent.
Pseudomonas/Aeromonas .... Partial inhibition. If growth, colonies are blue.
Materials and Media:

25g seafood sample
225ml SPB in 250ml Schott bottle
TCBS agar
Stomacher machine
Stomacher bag
Weighing machine
Skalpel & Spatula
Streaking loop

Procedure:
A. One-step enrichment
1. Weigh 25 g of sample into a sterile stomacher bag.

2. Add 225ml of SPB into the stomacher bag.
3. Stomach for 2 minutes until it is homogenized.
4. Transfer the homogenate back into the Schott bottle and close the screw cap.
5. Incubate the homogenate at 37°C for 18 to 24 h.
6. Streak a loopful from the top 1 cm of the enriched sample onto TCBS agar.
7. Incubate the TCBS plates at 37°C overnight.
8. Observe the plates for presumptive V. parahaemolyticus colonies.
B. Two-step enrichment
1. Weigh 25g of sample into a sterile stomacher bag.

2. Add 225ml of TSB containing 3% NaCl into the stomacher bag.
4. Transfer the homogenate back into the Schott bottle and close the screw cap.
5. Incubate the homogenate at 37 °C for 6 h.
6. Pipette out 1 ml of the enriched sample into 9 ml of SPB prepared in universal bottle.
7. Incubate at 37°C for 18 to 24 h.
8. Streak a loopful of the enriched sample onto TCBS agar and incubate at 37°C overnight.
9. Observe the plates for presumptive V. parahaemolyticus colonies.

Quiz 1
1. What is the purpose of each of the following steps in this protocol for the isolation of Vibrio
parahaemolyticus?
a) Enrichment with SPB
b) Streak enriched sample onto TCBS agar
2. What are the limitations of TCBS agar as a selective and differentiating medium for the
isolation and identification of Vibrio parahaemolyticus?

Practical 2 : Isolation of Listeria monocytogenes using one-step

enrichment method
4. Isolate L. monocytogenes using standard enrichment method.
Introduction:
Listeria are Gram-positive, facultative anaerobic, non-spore-forming, rod-shaped bacteria
with a low G+C content. The genus consists of six species i.e. Listeria monocytogenes,
Listeria ivanovii, Listeria seeligeri, Listeria innocua, Listeria welshimeri and Listeria grayi;
of which only L. monocytogenes is the primary human pathogen although there have
been rare reports of illnesses caused by L. seeligeri, L. ivanovii and
L. innocua. L. monocytogenes is an opportunistic intracellular pathogen that has become
an important cause of human foodborne infections worldwide.
Foodborne listeriosis, caused by the pathogen L. monocytogenes, is a relatively rare but

serious disease with high fatality rates (20–30%) compared with other foodborne
microbial pathogens, such as Salmonella. While L. monocytogenes causes a relatively
mild gastroenteritis in healthy adults, the illness can be severe in susceptible individuals.
Basically, L. monocytogenes most often affects those with a severe underlying disease
or condition (e.g. immunosuppression, HIV/AIDS, chronic conditions such as cirrhosis
that impair the immune system); pregnant women; unborn or newly delivered infants; and
the elderly. Symptoms range from flu-like illness to severe complications including
meningitis, septicaemia, spontaneous abortion or listeriosis of the newborn. The Listeria
species are tolerant to extreme conditions such as low pH, low temperature and high salt
conditions. Therefore they can be found in a variety of environments, including soil,
sewage, silage, water, effluents and foods. With globalization and increased
consumption of manufactured ready-to-eat foods

throughout the world, it is hardly surprising that L. monocytogenes has become

recognized as an important opportunistic human foodborne pathogen.
Most regulatory agencies stipulate that isolation must be capable of detecting one Listeria
organism per 25 g of food. This can only be achieved through enrichment methods that
employ antimicrobial agents to suppress competing microflora, prior to plating onto
selective agars and confirmation of cultures. Listeria isolation media also contains esculin
as all Listeria spp. hydrolyze esculin and the inclusion of esculin and ferric ion in
enrichment or plating media results in the formation of an intense black colour. This is
due to the formation of a complex between ferric iron with 6,7- dihydroxycoumarin, the
product of esculin cleavage by β-D-glucosidase, resulting in a black precipitate.

25g poultry sample
Stomacher bag
225ml Buffered Listeria Enrichment Broth (BLEB) in Schott bottle
Stomacher machine
PALCAM agar
Procedure:
C. One-step enrichment
1. Cut sample into small pieces, then place a 25g portion of sample into a sterile
stomacher bag.
2. Add 225ml of BLEB into the stomacher bag.
4. Transfer the homogenate back into the Schott bottle.
5. Incubate the homogenate at 30°C for 48 h.
6. Streak a loopful from the top 1cm of the enriched sample onto PALCAM agar.

7. Incubate the plates at 30°C for 48 h.

8. Observe the plates for presumptive L. monocytogenes colonies (black with grey
zone).

Quiz 2
What is the purpose of each of the following media in this protocol?

a) BLEB
b) PALCAM agar

Practical 3 : Isolation of Escherichia coli O157:H7 using one-step and two-

step enrichment methods
1. Isolate E. coli O157:H7 using standard enrichment method.
3. Understand the difference between using one-step and two-step enrichment methods.
Introduction:
Escherichia coli are among predominant species of facultative anaerobes in the human gut and
usually harmless to the host; however, a group of pathogenic E. coli has emerged and caused
diarrheal disease in humans. Referred to as diarrheagenic E. coli or commonly as pathogenic E.
coli, these groups are classified based on their unique virulence factors and can only be identified
by these traits. Hence, analysis for pathogenic E. coli often requires that the isolates be first
identified as E. coli before testing for virulence markers.
There are four recognized classes of enterovirulent E. coli that cause gastroenteritis in humans.
The pathogenic groups includes enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC),
enterohemorrhagic E. coli (EHEC), enteroinvasive E. coli (EIEC), enteroaggregative E. coli
(EAEC), diffusely adherent E. coli (DAEC) and perhaps others that are not yet well characterized.
Of these, only the first 4 groups have been implicated in food or water borne illness.
Enterohemorrhagic (EHEC) strain designated E. coli O157:H7 makes up one of the four classes.
E. coli serotype O157:H7 is a rare variety of E. coli that produces large quantities of one or more
related, potent toxins that cause severe damage to the lining of the intestine. E. coli O157:H7
infections often cause severe bloody diarrhoea and abdominal cramps. The infection can also
cause a complication called Haemolytic Uremic Syndrome (HUS). The toxins destroy red blood
cells and can lead to kidney failure.
About 2 – 7% of infections lead to HUS, particularly in children below the age of 5 and the elderly.
The first major outbreak of E. coli O157:H7 was in 1982, and traced to contaminated

hamburgers. Other known sources of infection include sprouts, lettuce, salami, unpasteurized
milk, juice and/or swimming in or drinking contaminated water.

25g poultry or beef sample
225ml tryptic soy broth (TSB) in Schott’s bottle
9ml mTSB (TSB supplemented with 0.2% Novobiocin)
CHROMagar E. coli O157:H7
Stomacher bag
Stomacher machine
1000µl tips
Micropippette
Inoculating loop
Bunsen burner
Procedure:
A. One-step enrichment
1. Cut sample into small pieces, then place a 25g portion of sample into a sterile stomacher
bag.
2. Add 225ml of TSB into the stomacher bag.
4. Transfer the homogenate back into the Schott’s bottle.
5. Incubate the homogenate at 37°C for 18 to 24h.
6. Streak a loopful of the enriched sample onto CHROMagar E. coli O157:H7.
7. Incubate the plates at 37°C for 18 to 24h.
8. Observe the plates for presumptive E. coli O157:H7 colonies (mauve purple).

B. Two-step enrichment
1. Cut sample into small pieces, then place a 25g portion of sample into a sterile stomacher
bag.
2. Add 225ml of TSB into the stomacher bag.
4. Transfer the homogenate back into the Schott bottle.
5. Incubate the homogenate at 37°C for 18 to 24h.
6. Transfer 1ml of the enriched sample into 9ml mTSB aseptically.
7. Incubate the suspension at 37°C for 18 to 24h.
8. Streak a loopful of the suspension onto CHROMagar E. coli O157:H7.
9. Incubate the plates at 37°C for 18 to 24h.
10. Observe the plates for presumptive E. coli O157:H7 colonies (mauve purple).

Quiz 3
1. What is the purpose of each of the following media in this protocol?

i. TSB
ii. mTSB
iii. CHROMagar E. coli O157:H7

Practical 4 : Extraction of DNA from human cheek cells by spooling
By the end of this experiment, students should be able to
1. isolate and visualize their own DNA
2. understand the basics of DNA structure and function
3. understand the principles of the steps needed to isolate DNA from human cells
Introduction:
Although DNA from a single cell can be extracted and studied, it's not enough to see with the
naked eye. To get a quantity sufficient for spooling, the more cells you have to work with the better
(many millions). Exact protocols vary considerably to account for the unique characteristics of
specific samples, but the general steps are homogenization, lysis, digestion, separation and
collection. The procedure is best carried out in a small (depending on the size of the sample)
glass or plastic tube.
A sample is generally blended or ground-up to thoroughly separate the cells from each other. This
makes the cell ingredients more accessible to the reagents that follow. Detergent or enzymes are
then added to the homogenate to lyse the cell membranes (and nuclear membranes if the cells
are eukaryotic) to free the DNA. At this point, the DNA is surrounded by proteins, lipids,
carbohydrates: everything else that was contained in the cells.
A further enzymatic digestion may be necessary to break down proteins so they do not bind to
DNA and interfere with its collection. DNA is separated from the rest of the cell contents by adding
cold, pure, ethyl or isopropyl alcohol. DNA is not soluble in these alcohols so it will condense to
try to minimize its contact with the alcohol. The condensed DNA is then collected, usually by
centrifugation or spooling. DNA collection by spooling is effective when a large amount of DNA is
obtained from an extraction procedure. It is also an excellent demonstration method since
an impressive tangle of pure DNA is clearly visible.
To spool DNA the separation step must be carried out carefully. If it wasn't a part of the lysis
reagent mixture previously added, a concentrated salt solution (sodium chloride) must be added
to the solution before the alcohol addition step. The cold alcohol is slowly poured down the side

of the test tube to form a layer on top of the aqueous solution, avoiding mixing. If done correctly,
the alcohol will form its own layer on top of the salty layer.
To collect the DNA from the salty layer, carefully place a glass stir rod though the alcohol layer
until it touches the bottom of the tube. Slowly spin the rod between the fingers, while watching the
interface between the two layers. If enough DNA is present, it will clump together at the interface
between layers to form a milky translucent mass. Spin the rod to wrap the DNA around it (that is
the spooling part) and pull it out of the tube. The DNA can be transferred to another tube of pure
alcohol for storage or further analysis.

50 ml tube 10 ml 0.9% sodium chloride (NaCl) solution
2 ml tube 10 ml 50% liquid dishwashing detergent
5 ml pipette and tips 5 ml 95% ethanol
Stirring rod
Procedure:
A. Collection of cheek cells
1. Measure 10 ml of 0.9% NaCl into a cup.

2. Rinse your mouth with the salt solution for 60 seconds.
3. Expel the salt solution, now containing cheek cells, into a 50 ml tube.
4. Discard the cup.

B. Isolation of cheek cell DNA by spooling
1. Pour about 10 ml of 50% detergent solution into the cheek cell suspension.
2. Cap and mix well by gently inverting the tube. Do not shake the tube.
3. Using a pipette, carefully layer about 5 ml of 95% ethanol on top of the suspension of
lysed cells by allowing the alcohol to run down the side of the tube. The alcohol should
form a distinct layer on top of the detergent and cell mixture.
4. Insert a glass rod through the ethanol into the cell suspension. Gently stir and roll the rod
between your fingers, in one direction, but do not mix the two-layers.
5. Observe the glass rod. DNA will appear as a slimy white mass adhering to the rod.

Quiz 4
1. What is the purpose of each of the following components in this protocol?

a) Detergent
c) Salt
c) Ethanol

Practical 5 : Extraction of genomic DNA from bacteria
6. Extract DNA from bacterial culture using boiled-cell method.
7. Understand the basic principles in DNA extraction.
Introduction:
Deoxyribonucleic acid (DNA) is the genetic information molecule for all non-viral life-
forms on Earth. DNA contains coded sequences that specify the structure of ribonucleic
acid (RNA) and proteins. DNA is organized into units called genes, each of which codes
for a particular RNA or protein sequence. Genes are studied to learn about biological
structure and function, evolution, disease and many other aspects of living systems. To
study genes in detail, DNA must be isolated and purified from cells of interest.
DNA isolation is a routine procedure to collect DNA for subsequent molecular or forensic
analysis. There are three basic and one optional step in a DNA extraction:
1. Break the cells open, which commonly referred to as cell disruption or cell lysis, in
order to expose the DNA within. This is commonly achieved by grinding or
sonicating the sample.
2. Removal of membrane lipids by adding a detergent.
3. Removal of proteins by adding a protease (optional but almost always done).
4. Precipitation of the DNA with an alcohol — usually ice-cold ethanol or isopropanol.
Since DNA is insoluble in these alcohols, it will aggregate together, giving a pellet
upon centrifugation. This step also removes alcohol-soluble salt.
Refinements of the technique include adding a chelating agent to sequester divalent

cations such as Mg2+ and Ca2+. This stops dnase enzymes from degrading the DNA.
Cellular and histone proteins bound to the DNA can be removed either by adding a
protease or by having precipitated the proteins with sodium or ammonium acetate, or

extracted them with a phenol-chloroform mixture prior to the DNA-precipitation. If desired,

the DNA can be resolubilized in a slightly alkaline buffer or in ultra-pure water.
DNA concentration can be determined measuring the intensity of absorbance of the

solution at the 600 nm with a spectrophotometer and comparing to a standard curve of
known DNA concentrations. Measuring the intensity of absorbance of the DNA solution
at wavelengths 260 nm and 280 nm is used as a measure of DNA purity. DNA absorbs
UV light at 260 and 280 nanometres, and aromatic proteins absorb UV light at 280 nm; a
pure sample of DNA has the 260/280 ratio at 1.8 and is relatively free from protein
contamination. A DNA preparation that is contaminated with protein will have a 260/280
ratio lower than 1.8.
DNA can be quantified by cutting the DNA with a restriction enzyme, running it on an
agarose gel, staining with ethidium bromide or a different stain and comparing the
intensity of the DNA with a DNA marker of known concentration.

Pure culture of Escherichia coli 1000 µl tips
Tryptic Soy Broth (TSB) 1.5 ml microcentrifuge tube
Inoculating loop Centrifuge machine
Sterile distilled water Waterbath/Heating block
1000 µl micropipette Ice/Freezer

Procedure:
A. Bacterial inoculation
1. Inoculate a loopful of pure E. coli culture into TSB.

2. Incubate at 37°C for 18-24h.
B. DNA Extraction
1. Transfer the overnight broth culture of E. coli into a 1.5 ml microcentrifuge tube.
2. Centrifuge the tube at 12,000 rpm for 1 minute.
3. Discard the supernatant and keep the pellet.
4. Add 500 µl of sterile distilled water to the pellet and resuspend.
5. Boil the suspension for 10 minutes.
6. After boiling, immediately cool at -20°C for 10 minutes.
7. Centrifuge the suspension at 12,000 rpm for 3 minutes.
8. Transfer the supernatant (which is the DNA) into a new microcentrifuge tube and
keep at -20°C for further use.

Quiz 5
3. What is the purpose of each of the following steps in this protocol?

c) Centrifugation of broth culture
d) Boiling
e) Immediate cooling


Practical 6 : Identification of pathogen using Polymerase Chain Reaction

(PCR)
1. understand the steps to extract DNA of E. coli O157:H7
2. understand the principles of PCR
Introduction:
Since its introduction in 1987, polymerase chain reaction (PCR) technology has been proven to
be instrumental for the detection of pathogens in food. The PCR represents a rapid procedure
with both high sensitivity and specificity for the immediate detection and identification of specific
pathogenic bacteria from different food materials.
The polymerase chain reaction (PCR) is used to amphfy a segment of DNA that lies between two
regions of known sequence (I-3). It requires two ohgonucleotide primers that flank the DNA
fragment to be amplified and employs repeated cycles of heat denaturation of the DNA, annealing
of the primers to their complementary sequences, and extension of the annealed primers with a
thermostable DNA polymerase (4). These primers typically have different sequences, are
complementary to sequences that lie on opposite strands of the template DNA, and flank the
segment of DNA that 1s to be amplified. Since the extension products themselves are also
complementary to and capable of binding primers, successive cycles of amplification essentially
double the amount of target DNA synthesized in the previous cycle. The efficacy of PCR is
measured by its specificity, efficiency (i.e., yield and length of PCR product), and fidelity (5). A
highly specific PCR will generate one, and only one, amplification product that 1s the intended
target sequence. More efficient amplification will generate more products m fewer cycles or will
produce longer PCR products. A highly accurate (i.e., high fidelity) PCR will contain a negligible
amount of DNA polymerase-induced errors in its product.
In molecular biology, the polymerase chain reaction (PCR) is a technique to amplify a single or
few copies of a piece of DNA across several orders of magnitude, generating thousands to
millions of copies of a particular DNA sequence. The method relies on thermal cycling, consisting
of cycles of repeated heating and cooling of the reaction for DNA melting and

enzymatic replication of the DNA. Primers (short DNA fragments) containing sequences
complementary to the target region along with a DNA polymerase (after which the method is
named) are key components to enable selective and repeated amplification. As PCR progresses,
the DNA generated is itself used as a template for replication, setting in motion a chain reaction
in which the DNA template is exponentially amplified. PCR can be extensively modified to perform
a wide array of genetic manipulations.
Figure 1: Mechanisms of DNA amplification by PCR: Strand 1 and Strand 2 are the original DNA
strands. The short dark grey fragments are the primers. After multiple heating and cooling
cycles, the original strands remain, but most of the DNA consists of amplified copies of the
segment (shown in lighter grey) synthesized by the heat stable DNA polymerase. Source:
Polymerase Chain Reaction: Principles and Uses of PCR | MEDCHROME)
Almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase, an
enzyme originally isolated from the bacterium Thermus aquaticus. This DNA polymerase
enzymatically assembles a new DNA strand from DNA building blocks, the nucleotides, by using
single-stranded DNA as a template and DNA oligonucleotides (also called DNA primers), which
are required for initiation of DNA synthesis. The vast majority of PCR methods use thermal

cycling, i.e., alternately heating and cooling the PCR sample to a defined series of temperature
steps. These thermal cycling steps are necessary first to physically separate the two strands in a
DNA double helix at a high temperature in a process called DNA melting. At a lower temperature,
each strand is then used as the template in DNA synthesis by the DNA polymerase to selectively
amplify the target DNA. The selectivity of PCR results from the use of primers that are
complementary to the DNA region targeted for amplification under specific thermal cycling
conditions.
i. Initialization step: This step consists of heating the reaction to a temperature of 94–96 °C
(or 98 °C if extremely thermostable polymerases are used), which is held for 1–9 minutes.
It is only required for DNA polymerases that require heat activation by hot-start PCR.
ii. Denaturation step: This step is the first regular cycling event and consists of heating the
reaction to 94–98 °C for 20–30 seconds. It causes DNA melting of the DNA template by
disrupting the hydrogen bonds between complementary bases, yielding single strands of
DNA.
iii. Annealing step: The reaction temperature is lowered to 50–65 °C for 20–40 seconds
allowing annealing of the primers to the single-stranded DNA template. Typically the
annealing temperature is about 3-5 degrees Celsius below the Tm of the primers used.
Stable DNA-DNA hydrogen bonds are only formed when the primer sequence very closely
matches the template sequence. The polymerase binds to the primer-template hybrid and
begins DNA synthesis.
iv. Extension/elongation step: The temperature at this step depends on the DNA polymerase
used; Taq polymerase has its optimum activity temperature at 75–80 °C, and commonly
a temperature of 72 °C is used with this enzyme. At this step the DNA polymerase
synthesizes a new DNA strand complementary to the DNA template strand by adding
dNTPs that are complementary to the template in 5' to 3' direction, condensing the 5'-
phosphate group of the dNTPs with the 3'-hydroxyl group at the end of the nascent
(extending) DNA strand.
v. Final elongation: This single step is occasionally performed at a temperature of 70– 74
°C for 5–15 minutes after the last PCR cycle to ensure that any remaining single- stranded
DNA is fully extended.
vi. Final hold: This step at 4–15 °C for an indefinite time may be employed for short-term
storage of the reaction.

A basic PCR set up requires several components and reagents. These components include:
• DNA template that contains the DNA region (target) to be amplified.
• Two primers that are complementary to the 3' (three prime) ends of each of the sense and
anti-sense strand of the DNA target.
• Taq polymerase or another DNA polymerase with a temperature optimum at around 70
°C.
• Deoxynucleoside triphosphates (dNTPs; also very commonly and erroneously called
deoxynucleotide triphosphates), the building blocks from which the DNA polymerases
synthesizes a new DNA strand.
• Buffer solution, providing a suitable chemical environment for optimum activity and stability
of the DNA polymerase.
• Divalent cations, magnesium or manganese ions; generally Mg2+ is used, but Mn2+ can be
utilized for PCR-mediated DNA mutagenesis, as higher Mn2+ concentration increases the
error rate during DNA synthesis.
• Monovalent cation potassium ions.
The PCR usually consists of a series of 20 to 40 repeated temperature changes called cycles;
each cycle typically consists of 2-3 discrete temperature steps. The temperatures used and the
length of time they are applied in each cycle depend on a variety of parameters. These include
the enzyme used for DNA synthesis, the concentration of divalent ions and dNTPs in the reaction,
and the melting temperature (Tm) of the primers. To check whether the PCR generated the
anticipated DNA fragment (also sometimes referred to as the amplimer or amplicon), agarose gel
electrophoresis is employed for size separation of the PCR products. The size(s) of PCR products
is determined by comparison with a DNA ladder (a molecular weight marker), which contains DNA
fragments of known size, run on the gel alongside the PCR products (this will be covered in
Practical 7).
Materials and Methods:

Materials:
Overnight culture of E. coli O157: H7 5X PCR buffer
Sterile distilled water Taq polymerase
Heating block dNTP mix
1.5 ml tubes MgCl2

0.2 ml tubes Forward and reverse primer

1000 µl tips DNA template
100 µl tips Gel electrophoresis set
10 µl tips 0.5X TBE buffer
Micropipettes 100 bp DNA ladder
PCR thermocycler
Procedures:
A. Polymerase Chain Reaction (PCR)
1. Using the DNA extract from previous experiment, perform PCR amplification in a 25 µl
reaction mixture containing:
Initial conc. Final conc. Final volume

sdH2O - - 12.9 µl
5X PCR buffer 5X 1X 4.0 µl
MgCl2 25 mM 2.5 mM 2.5 µl
dNTP mix 10 mM 0.2 mM 0.5 µl
Forward primer 10 µM 0.4 µM 1.0 µl
Reverse primer 10 µM 0.4 µM 1.0 µl
Taq polymerase 5 U/µl 0.5 U/µl 0.1 µl
DNA - - 2.0 µl
TOTAL 25.0 µl

2. Use the following thermocycler conditions:
Steps Temperature Time

Pre-denaturation 94°C 2 min
Denaturation 94°C 1 min
Annealing 55°C 1 min 35 cycles
Extension 72°C 1 min
Final extension 72°C 10 min
Hold 4°C ∞
3. The PCR products, or amplicons, will be run on gel electrophoresis to visualize the PCR
product. This will be covered in Practical 7. The expected size of the PCR product is 625
bp.

Quiz 6
1. What is the purpose of each of the following components in this protocol?

a) DNA extract
b) Primers
d) Taq polymerase
2. Please identify problems/ limitation of PCR for the detection of pathogenic bacteria in
food.

Practical 7 : Visualisation of PCR amplicons by gel electrophoresis
1. Detect the presence of bacterial cell DNA or PCR products using gel electrophoresis.
2. Understand the basic concepts of gel electrophoresis.
Introduction:
Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid (DNA),
ribonucleic acid (RNA), or protein molecules using an electric field applied to a gel matrix. DNA
gel electrophoresis is usually performed for analytical purposes, often after amplification of DNA
via PCR, but may be used as a preparative technique prior to use of other methods such as mass
spectrometry, RFLP, PCR, cloning, DNA sequencing, or Southern blotting for further
characterization.
The term "gel" in this instance refers to the matrix used to contain, and then separate the target
molecules. In most cases, the gel is a crosslinked polymer whose composition and porosity is
chosen based on the specific weight and composition of the target to be analyzed. When
separating proteins or small nucleic acids (DNA, RNA, or oligonucleotides) the gel is usually
composed of different concentrations of acrylamide and a cross-linker, producing different sized
mesh networks of polyacrylamide. When separating larger nucleic acids (greater than a few
hundred bases), the preferred matrix is purified agarose. In both cases, the gel forms a solid, yet
porous matrix. Acrylamide, in contrast to polyacrylamide, is a neurotoxin and must be handled
using appropriate safety precautions to avoid poisoning. Agarose is composed of long
unbranched chains of uncharged carbohydrate without cross links resulting in a gel with large
pores allowing for the separation of macromolecules and macromolecular complexes.
"Electrophoresis" refers to the electromotive force (EMF) that is used to move the molecules
through the gel matrix. By placing the molecules in wells in the gel and applying an electric field,
the molecules will move through the matrix at different rates, determined largely by their mass
when the charge to mass ratio (Z) of all species is uniform, toward the anode if negatively charged
or toward the cathode if positively charged.

After the electrophoresis is complete, the molecules in the gel can be stained to make them
visible. Ethidium bromide, an intercalating dye may be used for this process. Other methods may
also be used to visualize the separation of the mixture's components on the gel. If the analyte
molecules fluoresce under ultraviolet light, a photograph can be taken of the gel under ultraviolet
lighting conditions. If the molecules to be separated contain radioactivity added for visibility, an
autoradiogram can be recorded of the gel.
If several mixtures have initially been injected next to each other, they will run parallel in individual
lanes. Depending on the number of different molecules, each lane shows separation of the
components from the original mixture as one or more distinct bands, one band per component.
Incomplete separation of the components can lead to overlapping bands, or to indistinguishable
smears representing multiple unresolved components.
Bands in different lanes that end up at the same distance from the top contain molecules that
passed through the gel with the same speed, which usually means they are approximately the
same size. There are molecular weight size markers available that contain a mixture of molecules
of known sizes. If such a marker was run on one lane in the gel parallel to the unknown samples,
the bands observed can be compared to those of the unknown in order to determine their size.
The distance a band travels is approximately inversely proportional to the logarithm of the size of
the molecule.
Gel electrophoresis is used in forensics, molecular biology, genetics, microbiology and

biochemistry. The results can be analyzed quantitatively by visualizing the gel with UV light and
a gel imaging device. The image is recorded with a computer operated camera, and the intensity
of the band or spot of interest is measured and compared against standard or markers loaded on
the same gel. The measurement and analysis are mostly done with specialized software.
Materials:
DNA extract (from previous experiment) Ethidium bromide
Agarose powder 100 µl & 10 µl micropipettes
0.5X Tris-Base-EDTA (TBE) buffer 100 µl & 10 µl pipette tips
Hotplate Stirrer/Microwave Oven Gel electrophoresis set

Gel casting set Gel Documentation System

DNA marker 250 ml conical flask
Loading dye
Procedure:
Gel Electrophoresis
1. Weigh 1 g of agarose powder into 250 ml conical flask.

2. Mix with 100 ml of 0.5X TBE buffer to make 1% agarose.
3. Heat until it is fully dissolved.
4. Let it cool and then add with 1 µl of ethidium bromide.
5. Pour the agarose into gel casting set and let it solidify.
6. Load DNA sample and DNA marker into the wells
7. Run at 100 V for 30 minutes.
8. View the gel using Gel Documentation System.

Quiz 7:
What is the purpose of each of the following components in this protocol?
a) Ethidium bromide
b) TBE buffer
c) Agarose

Practical 8 : Designing oligonucleotides (primers) for PCR
1. calculate the Tm of an oligonucleotide
2. describe factors that affect oligonucleotide binding and function
3. manually design primers with computer analysis assistance
Introduction:
Good primer design is essential for a successful PCR reaction. There are many factors to take
into account when designing the optimal primers for your gene of interest. Here are some tips to
consider when designing primers.
1. In general, a length of 18–30 nucleotides for primers is good.

2. Try to make the melting temperature (Tm) of the primers between 65°C and 75°C, and within
5°C of each other.
3. If the Tm of your primer is very low, try to find a sequence with more GC content, or extend
the length of the primer a little.
4. Aim for the GC content to be between 40 and 60%, with the 3' of a primer ending in C or G
to promote binding.
5. Typically, 3 to 4 nucleotides are added 5’ of the restriction enzyme site in the primer to allow
for efficient cutting.
6. Try to avoid regions of secondary structure, and have a balanced distribution of GC-rich and
AT-rich domains.
7. Try to avoid runs of 4 or more of one base, or dinucleotide repeats (for example, ACCCC or
ATATATAT).
8. Avoid intra-primer homology (more than 3 bases that complement within the primer) or inter-
primer homology (forward and reverse primers having complementary sequences). These
circumstances can lead to self-dimers or primer-dimers instead of annealing to the desired
DNA sequences.
An oligonucleotide is a short nucleic acid polymer, typically with twenty or fewer bases. Although
they can be formed by bond cleavage of longer segments, they are now more commonly
synthesized by polymerizing individual nucleotide precursors. Automated synthesizers allow the

synthesis of oligonucleotides up to 160 to 200 bases. The length of the oligonucleotide is usually
denoted by "mer" (from Greek meros, "part"). For example, a fragment of 25 bases would be
called a 25-mer. Because oligonucleotides readily bind to their respective complementary
nucleotide, they are often used as probes for detecting DNA or RNA.
Examples of procedures that use oligonucleotides include DNA microarrays, Southern blots, ASO
analysis, fluorescent in situ hybridization (FISH), and the synthesis of artificial genes.
Oligonucleotides composed of DNA (oligodeoxyribonucleotides) are often used in the polymerase
chain reaction, a procedure that can greatly amplify almost any small piece of DNA. There, the
oligonucleotide is referred to as a primer, allowing DNA polymerase to extend the oligonucleotide
and replicate the complementary strand.
A primer is used in many molecular techniques from PCR to DNA sequencing. These primers are
designed to have a sequence which is the reverse complement of a region of template or target
DNA to which we wish the primer to anneal.
Materials:
Computer with internet access
Web browser (such as Internet Explorer)
USB stick
Procedure:
A. Obtaining the HIV sequence to be amplified
1. Locate the National Center for Biotechnology Information (NCBI)
(http://www.ncbi.nlm.nih.gov/).
2. Select “Search Nucleotide” for “K02007”. Select “Search”.
3. What information can be obtained when searching for a specific accession number?

4. Copy the nucleotide sequence from positions 1400 to 1800.

5. Open a word-processing file and paste the sequence into it. Save the document.
B. Manual design of PCR oligonucleotide primer pair

1. Open the word-processing file that contains the sequence.
2. Find and highlight the positions 1551 through 1665.
3. Study the highlighted gag gene sequence and its neighboring codons.
4. Write/type in the complimentary strand beneath it.
5. Construct a forward primer and a reverse primer to amplify this sequence using the
following criteria:
• Primer length = 20 nucleotides
• Melting temperature (Tm) = 55 to 59°C
• Avoid hairpin loops
• Avoid long repeats of a single base
• Avoid complimentary between the forward and reverse primer, especially at the 3’
ends
• Aim for 50% to 60% G+C content
6. Calculate the Tm using the following formulas:
• Tm = [4(G+C) + 2(A+T)] °C
• Tm = 69.3°C + 0.41[%(G+C) – 650/l, where l is the length of the primer
7. Write your primers.
a) Forward primer:
b) Reverse primer:
C. Computer-assisted oligonucleotide primer design

1. Open the NCBI webpage that contains the nucleotide sequence position 1400 to 1800.
2. Highlight and copy the sequence.
3. Click on the link “Pick Primers”.
4. Enter your sequence in the PCR template box by copying and pasting. Delete any
numerals.
5. Adjust any necessary parameters (if any).
6. At the bottom of the page, select “Get Primers”.
7. Examine and choose a primer pair as instructed on the results page. You may select or
deselect any of the available analysis tools.

8. Copy your selected primer pairs.

a) Forward primer:
b) Reverse primer:

Practical 9 : : Diagnostic method for the detection of food allergens –

quantitative determination of total soluble proteins using Bradford assay.
Objectives:
1. To determine the concentration of total soluble proteins in samples using Bradford
assay.
2. To identify the suitability of protein assays for measuring the protein concentration of
samples.
3. To determine whether the extraction buffers affect the solubility of proteins.
Introduction
Detection of allergens in food is critical in order to protect allergic consumers from allergen
exposure and ensure compliance with regulatory policies on food allergen labelling. Several rapid
and effective methods have been successfully utilised for the detection of allergens in food
including PCR assay and mass spectrometry but immunoassay such as enzyme-linked
immunosorbent assay (ELISA) is more commonly used for the detection of allergens in food
products due to its high sensitivity, cost effectiveness, and accuracy. ELISA methods require
effective solubilisation of the allergenic proteins in an extraction buffer prior to detection (Lasekan
& Nayak, 2016).
However, under food processing effect, the solubility of proteins may be decreased by the
formation of insoluble complexes (i.e. protein aggregates). This may cause an underestimation of
total concentration of allergens detected in processed food due to reduced solubility of proteins
in the buffer. To determine whether or not the solubility of protein is reduced after food processing
(which in this case, boiling), we are going to compare the concentration of total crude protein
extracts from boiled and raw milks.
Total protein assays are used to analyse hundreds of industrial, agricultural, and biotechnology
products. They are also basic for research purposes, especially for determining the specific
activity (i.e., total activity/total protein) of proteins, enzymes, antibodies, and lectins. Clearly,
accuracy and precision of specific activity measurements depend as much on accurate
measurement of total protein as on determination of total activity. In performing total protein
assays, there are five issues of concern:
(1) Sensitivity and technique of the method

(2) Clear definition of units
(3) Interfering compounds

(4) Removal of interfering substances before assaying samples

(5) Correlation of information from various techniques.
Many assays for quantifying total protein exist. Several are reliable and straightforward. How to
choose the most suitable or optimal method is a recurring problem; the solution frequently
requires the use of more than one method or protocol. A good strategy is to compare the results
of two methods, such as A280 measurements and one of the copper-based chromogenic
methods-assays that rely on different chemical properties. Very large differences in total protein
estimates from two or more methods occur with crude preparations from food extracts, which
may be laden with interfering substances. The principle question is often not how sensitive a
particular protein assay happens to be, but rather how the assay is affected by interfering
substances. The primary concern is how to manoeuvre around the interfering compounds or how
to eliminate them altogether, using analytical protocols to follow the progress (Lovrien & Matulis,
2005).
Table: Assays to quantify total protein and their interfering compounds (Lovrien & Matulis, 2005).
Assay Interfering compounds
Biuret Ammonium sulfate

Glucose
Sulfhydryl compounds
Sodium phosphate
Hartree Lowry EDTA

Guanidine-HCI
Triton X-100
SDS
Brij 35
>0.1 M Tris
Ammonium sulfate
1 M sodium acetate
1 M sodium phosphate
Bicinchoninic acid (BCA) EDTA

>10 mM sucrose or glucose
1.0 Mglycine
>5% ammonium sulfate
2 M sodium acetate
1 M sodium phosphate
Acid digestion-ninhydrin Ammonium sulfate
Amino sugars
UV adsorption Pigments
Phenolic compounds
Organic cofactors

Bradford >0.5% Triton X-100

>0.1% SDS
Sodium deoxycholate
Dry weigh All buffer salts
For this practical, we will only use Bradford assay to quantify total protein concentration in
solution. The Bradford Reagent can be used to determine the concentration of soluble proteins.
The procedure is based on the formation of a complex between the dye, Brilliant Blue G, and
proteins in solution. The protein-dye complex causes a shift in the absorption maximum of the
dye from 465 to 595 nm. The amount of absorption is proportional to the protein present. The
Bradford Reagent requires no dilution and is suitable for micro, multi-well plate, and standard
assays. The linear concentration range is 0.1-1.0 mg/ml of protein, using BSA (bovine serum
albumin) as the standard protein.
Figure 1: Reaction schematic of Commassie Brilliant Blue G-250 dye binding to basic (i.e.
arginine) and aromatic amino acid residues
The Bradford Reagent is compatible with reducing agents, which are often used to stabilize
proteins in solution. Other protein assay procedures (Lowry and BCA) are not compatible with
reducing agents. The Bradford Reagent should be used in place of these protein assays if
reducing agents are present. However, the Bradford Reagent is only compatible with low
concentrations of detergents. If the protein sample to be assayed has detergents present in the
buffer, it is suggested to use the BCA protein determination procedure.

Materials and methods

Samples - cow’s milk
Phosphate buffered saline (PBS) pH 7.4
Extraction buffer A: 1 x PBS (pH 7.2)
Extraction buffer B: Solubilisation buffer (1 x PBS with 0.5% SDS and 2% beta
mercaptoethanol, pH 7.2)
BSA stock in PBS (0.5 mg/ml) (for standards)
Bradford reagent (Bio-Rad)
1.5 mL microfuge tubes
2.0 mL microfuge tubes
96 well polystyrene plate
1 mL pipettor
200 uL pipettor
20 uL pipettor
Pipette tips
Microplate reader
Protocols
SAMPLE PREPARATION
A. Skim milk recovery
1. Aliquot 2 mL of of full cream milk samples into 2 ml centrifuge tube.
2. Centrifuge tube at 4500 rpm for 30 min at 4°C.
3. Pipette the skim milk in between the fat layer and the pelleted cells (ca. 1.7 mL) and
transfer into a fresh 2 mL tube.
B. Protein extraction
1. Aliquot 0.5 mL of the skim milk sample into 2.0 mL tubes.
2. Add an equal volume (0.5 mL) of Solubilisation buffer (PBS (pH 7.2) containing 0.5%
sodium dodecyl sulphate (SDS) and 2% β-mercaptoethanol).
3. Vortex the mixture for 1 min.
4. Incubate the tubes at 30°C for 60 min.
5. Centrifuge the tubes at 13,000 rpm for 5 min at room temperature.
TOTAL SOLUBLE PROTEIN DETERMINATION

C. Total protein assay

1. Set of standards is created from a stock of protein whose concentration is known.

2. The Bradford values obtained for the standard are then used to construct a standard curve
to which the unknown values obtained can be compared to determine their concentration.
Use a protein as your standard that most closely resembles the protein you are assaying,
which in this case, bovine serum albumin (BSA).
3. For BSA, use 0 – 500 μg/mL as your standard curve concentration. Prepare a standard
curve of absorbance versus micrograms protein and determine amounts from the curve.
(refer to Table 1)
4. Standards: aliquot known concentrations of standard, i.e. 1 – 500 µg/mL BSA in a total
volume of 50 µL into 1.5 mL microfuge tubes. Make up to 50 µl with distilled water. Vortex
tubes to mix well.
Table 1
μg/mL BSA Volume of BSA- Volume of Buffer *Notes
Standard (0 5 mg/mL) (PBS) - µL
– µL
0 0 µL 50 µL reagent blank
25 2.5 µL 47.5 µL
50 5 μL 45 µL
100 10 µL 40 µL
200 20 µL 30 µL
300 30 µL 20 µL
400 40 µL 10 µL
500 50 µL 0 µL
5. Pipette 20 µL of each BSA-Standard into individual wells of a 96-well plate in duplicate.

6. Unknown samples: Pipette up to 20 µL of unknown samples into individual wells of a 96-
well plate. Do all determinations in duplicate.
7. Add 200 µL of Bradford Reagent into all wells containing standard or sample.
8. Incubate plate for 3-5 min at room temperature (do not leave samples for more than 30
min after adding Bradford Reagent).
9. Measure absorbance of the samples and standards at 595 nm (A595) without any prior
incubation.

RECORDING AND REPORTING DATA FOR TOTAL PROTEIN ANALYSIS
D. Standard Curve for Protein Measurements:

A series of tests were performed on some samples and the following measurements were
obtained using a spectrophotometer. Below is an example of A595 reading of your standard, BSA,
with known concentration:
Protein A595 A595
concentration reading reading
(mg/ml) - blank
0 0.332 0
50 0.354 0.022
100 0.373 0.041
200 0.445 0.113
300 0.496 0.164
400 0.55 0.218
500 0.574 0.242
1. Enter your data into Excel.

2. Normalise your absorbance reading by subtracting the A595 reading of your standards with
the A595 reading of the blank (0 mg/ml), which in the example above, 0.332 (if you have
replicates, average the A595 reading of the blank first).
3. Create a graph of the data that is appropriately titled and labelled (Include your name on
the graph). Select data of both protein concentration of BSA and absorbance reading
(A595) – blank and insert scatter plot graph.

4. Once you have plotted a scatter plot graph, you will see a distribution of data points in
almost a straight line. Right click on one of the point, and select ‘Add Trendline…’

5. For trendline options, choose ‘Linear’ regression, ‘display equation on chart’, and
‘display R-squared value’ on chart. (R-squared is a statistical measure of how close the
data are to the fitted regression line. The closer the value to 1, the better the model fits
your data. Acceptable values should be between 0.95-1.0).
0.3
0.25
0.2
y = 0.0026x - 4E-05
R² = 0.9876
0.15
0.1
0.05
20 40 60 80 100 120
-0.05
6. The equation generated is for linear regression:
y = mx + b,
Where:
y is the absorbance reading at 595 nm (A595)

m is the slope value

x is the concentration (mg/ml)
b is the y-intercept.
7. Rearrange the equation to find x = (y-b)/m. Use the equation to determine the protein
concentrations of your samples (don’t forget to normalise the absorbance reading by
subtracting A595 reading of samples with A595 reading of your blank).
Read more on Bradford assay:

1. Bradford, M.M. (1976) Anal. Biochem. 72:248
2. Spector, T. (1978) Anal. Biochem. 86:142
3. Read, S.M. and Northcote, S. (1981) Anal. Biochem. 116:53
References
Kato, S., Yagi, T., Kato, A., Yamamoto, S., & Akimoto, M. (2015). Interlaboratory Study of ELISA
Kits for the Detection of Egg. Journal of AOAC International, 98(3), 810–816.
https://doi.org/10.5740/jaoacint.14-219
Lovrien, R., & Matulis, D. (2005). Assays for total protein. Current Protocols in Microbiology,
Appendix 3, Appendix 3A. http://doi.org/10.1002/9780471729259.mca03as00
Vincent, D., Ezernieks, V., Elkins, A., Nguyen, N., Moate, P. J., Cocks, B. G., & Rochfort, S.
(2015). Milk Bottom-Up Proteomics: Method Optimization. Frontiers in Genetics, 6, 360.
http://doi.org/10.3389/fgene.2015.00360

Quiz 8
1. What is the purpose of protein determination in food analysis?
2. Why is it important to quantify soluble proteins before performing ELISA?
3. Identify factors that are affecting the sensitivity of Bradford assay for protein
determination.
4. What are the limitations of Bradford assay for protein determination?

Practical 10 : Detection of allergens in food samples using enzyme-linked

immunosorbent assay (ELISA)
Objectives:
1. To understand the application of ELISA for the detection of allergens in food
samples.
2. To quantitatively determine target antigen in a sample using indirect ELISA
3. To determine the specificity of antibody used for the detection of target antigens
4. To understand the application of ELISA as a rapid detection kit
Introduction
The indirect ELISA is one of many ELISA assay formats that can be used for the detection
and quantification of specific antigens in sample solution. The indirect ELISA method has
high sensitivity since more than one labelled secondary antibody can bind the primary
antibody; it is more economical than the direct ELISA as fewer labelled antibodies are
needed. Indirect ELISA delivers greater flexibility since different primary antibodies can
be used with a single labelled secondary antibody. Among its disadvantages is the
possibility of cross-reactivity of secondary antibody to the adsorbed antigen, which could
increase background noise. Also, indirect ELISA assays take longer to run than direct
ELISAs since an additional incubation step for the secondary antibody is required. The
indirect ELISA is most suitable for determining total antibody concentration in samples.

Figure 1: Principle of indirect ELISA

(Source: https://www.creative-diagnostics.com/ELISA-guide.htm)
Different Stages of Indirect ELISA:
Coating ELISA Plates:

Coating is achieved through passive adsorption of the antigen to the assay microplate.
This process occurs though hydrophobic interactions between the microtiter plate and
non-polar protein residues. Although individual proteins may require specific conditions
or pre-treatment for optimal binding, the most common method for coating plates involves
adding a 2-10 μg/mL solution of protein dissolved in an alkaline buffer such as phosphate-
buffered saline (pH 7.4), carbonate-bicarbonate buffer (pH 9.4) or other buffers that
increase the solubility of antigens. The buffer contains no other proteins that might
compete with the target antibody for attachment to the microtiter plate. Antigens, which
are protein in nature will attach passively to the microtiter well plate during incubation in
incubator at 30-370C. Selection of ELISA plate is crucial as you have to make sure to use
a specialised ELISA plate, which is a polystyrene plate that has been gamma-irradiated
to allow high binding of antigen via hydrophobic and ionic bonds.
Washing step:
After incubation any excess antigen is removed by washing steps by flooding and
emptying the wells with neutral phosphate buffered saline (PBS) with detergent (normally
we use Tween 20, a non-toxic polysorbate-type nonionic surfactant commonly

used as detergent and emulsifier). Washing steps are necessary to remove non-bound
reagents and decrease background, thereby increasing the signal-to-noise ratio.
Insufficient washing will allow high background, while excessive washing might result in
decreased sensitivity caused by elution of the antigen from the well.
Addition of blocking buffer:

The binding capacity of microplate wells is typically higher than the amount of protein
coated in each well and the residual binding capacity of the plate is blocked in this step.
The ideal blocking buffer will bind to all potential sites of non-specific interaction,
eliminating background altogether, without altering or obscuring the epitope for antibody
binding. The blocking buffer is effective if it improves the sensitivity of an assay by
reducing background signal and improving the signal-to-noise ratio. Bovine serum
albumin, an inert protein, has been shown to be most effective at blocking than any protein
tested. Other alternative blocking agents that are commonly used are skimmed milk,
caseins, and fish gelatin (to be quite honest, any protein that does not cross-react with
antibodies used in the ELISA can be used) and other commercial non-protein blocking
agents such as Superblock Blocking buffer (Thermo Scientific) or Super GTM Blocking
buffer (Grace Bio-Labs). Normally 1-2% BSA in PBS is used as a blocking buffer.
Coated plates can be used immediately or stored at 4°C for later use, depending on the
stability of the coated protein.
Washing step:
Excess antigen or unbound antigen are removed by washing step with PBS containing
0.5% Tween 20 (pH 7.4) and is followed by the addition of detection antibody.
Addition of a detection antibody

Next, an antibody specific to the antigen is added to the well of the plate. Normally, an
antibody developed for the use of immunoassays is immunoglobulin G (IgG) that has
been raised in animals (e.g. rat, hamster, rabbit, goat, chicken, etc.). The animal is
immunised by injecting it with the antigen for several times in a span of 6 months. The

animal is then bled and the serum is recovered from the blood. The IgG antibody is
separated and purified from the serum. IgG antibody may be produced as monoclonal or
polyclonal. Monoclonal antibody is a specific antibody that recognises only a single
epitope of the antigen. Polyclonal antibody, on the other hand, is a mixture of IgG
antibodies that recognise different epitopes on the same antigen (Figure 3). Detection
antibody must be able to bind specifically to the epitope(s) of the antigen. If monoclonal
antibody is used for the ELISA system, orientation of the protein binding on the plate
surface is crucial to ensure that the epitope is available for the binding with the antibody.
For indirect ELISA, polyclonal antibody is usually preferred (depends on the type of
study).
Figure 2: Structure of an IgG antibody

(Source: https://teaching.ncl.ac.uk/bms/wiki/index.php/Antibody)

Figure 3: Comparison between polyclonal and monoclonal antibodies
Addition of a secondary antibody –enzyme conjugate

The next step is the addition of antibody enzyme conjugate, diluted in PBS buffer directed
against the antigen. The choice of antibody enzyme conjugate is determined by the goals
of the assay. If it is necessary to detect all detection antibodies that bind to antigen,
conjugates prepared with antibodies specific for Ig κ and λ light chains of the detection
antibody should be used. Alternatively, protein A or protein G–enzyme conjugates may
be preferable when screening monoclonal antibodies. Such antibodies are produced
against immunoglobulins (Igs) of species in which the detecting antibodies are produced
and are termed anti-species conjugates. Thus, if detecting antibodies are produced in
rabbits, the enzyme-labeled antibodies would have to be anti-rabbit Igs in nature. This
allow greater flexibility in use of anti-species conjugates in that different specificities of
conjugate can be used to detect particular Igs binding in the assay. For example, the anti-
species conjugate could be anti- IgM, IgG1, IgG2 and so on. The enzyme can be linked
to a protein such as streptavidin if the primary antibody is biotin labelled. The most
commonly used enzyme labels horseradish peroxidase (HRP) and alkaline phosphatase
(AP). Other enzymes have been used as well, but they have not gained widespread
acceptance because of limited substrate options. These include β-

galactosidase, acetylcholinesterase and catalase. Fluorescent dye conjugate may also

be used for the detection. However, the limitation may be due to the lack of fluorescent
multi-channel plate reader in the laboratory as it is more expensive than the UV/Vis multi-
channel plate reader.
Figure 4: How secondary antibody-enzyme conjugate binds to the detection antibody
Washing step:
Unbound antibody enzyme conjugate is washed away after incubation phase.
Adding substrate:
Substrates are critical for the detection and visualization steps of an ELISA. The step
involves the addition of suitable substrate solution for the particular enzyme conjugated
to the antibodies. The objective is to allow development of color reaction through enzyme
catalysis. A large selection of substrates is available for performing the ELISA with an
HRP or AP conjugate. TMB (3, 3’, 5, 5’-tetramethyl benzidine) is the most commonly used
substrate for the enzyme horseradish peroxidase (HRP). The substrates of alkaline
phosphatase (AP), 4-methylumbelliferyl phosphate (MUP) and pNPP (p-Nitrophenyl-
phosphate) are nontoxic and relatively stable. Solutions of p-nitrophenyl phosphate
(NPP) are stable for months at 4°C, while solutions of 4- methylumbelliferyl phosphate
(MUP) can be kept for months at room temperature without any significant spontaneous
hydrolysis. The biggest disadvantage if NPP is used as a substrate is that, the yellow
color of the nitrophenyl product is relatively
difficult to detect visually. Using the substrate MUP instead of NPP can greatly enhance
the sensitivity of the assay. The fluorogenic system using MUP is 10 to 100 times faster
than the chromogenic system using NPP, and appears to be as sensitive as an enhanced
chromogenic assay in which alkaline phosphatase generates NAD+ from NADP. The
disadvantage of using fluorogenic substrates is that they require a microplate fluorometer
costing twice as much as a high quality microtitre plate spectrophotometer.
The choice of substrate depends upon the required assay sensitivity and the
instrumentation available for signal-detection (spectrophotometer, fluorometer or
luminometer)
Stop solution:
The reaction is allowed to progress for a defined period after which the reaction is stopped
by altering the pH of the system. Stop Solution is a used to terminate the enzyme
substrate reaction for ELISA applications after attaining the desired color intensity
which is an indication of analyte level. For e.g. The TMB substrate reacts with immobilized
horseradish peroxidase (HRP) conjugated antibodies to produce a blue solution. Reaction
may be stopped by 0.2 M sulphuric acid which offers a yellow end product read at 450
nm. AP stop solution (0.5M NaOH) does not change the yellow color or the absorbance
of the chromogen, and so the absorbance is read at 405 nm to 420 nm.
Quantification:
Specially designed spectrophotometers are available which reads through the microtiter
wells either singly or in rows. Several ELISA plate readers are available, with increasing
levels of sophistication. Some of these provide a measurement of optical density while
some tabulate data and apply statistical analysis. Compatibility with a small computer,
and availability of a suitable program to process the results and transform the optical
density readings into concentrations of protein are important additional things to look for
when selecting an instrument. Most ELISA readers can be set to measure the absorbance
of the colors produced by the action of antibody- conjugated enzymes on

their respective substrates. The microplate reader works by illuminating a particular type
of light at each of the samples in the microwell plate. Common detection modes for
microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved
fluorescence and fluorescence polarization. A light source illuminates the sample using a
specific wavelength (selected by an optical filter, or a monochromator), and a light
detector located on the other side of the well measures how much of the initial (100%)
light is transmitted through the sample, the amount of transmitted light will typically be
related to the concentration of the molecule of interest. This is called absorbtion detection.
The range of application of fluorescence intensity detection is much broader than when
using absorbance detection, but instrumentation is usually more expensive. Microplate
readers feed the absorbance or fluorescence measures into a computer program that
analyses the particular information being collected.
Assay optimization:
Serial dilution titration analyses are performed to determine optimal concentrations of
reagents to be used in ELISAs. All three reactants in ELISA, a solid-phase coating
reagent, a secondary reagent that binds the primary reagent and an enzyme-conjugated
tertiary developing reagent that binds to the secondary reagent are serially diluted and
analyzed by a criss-cross matrix analysis. Once the optimal concentrations of reagents to
be used under particular assay conditions are determined, these variables are kept
constant from experiment to experiment.
Assay validation:
ELISA kits that are commercially available which are used for diagnostic purposes in the
detection of specific antigen or antibody in the serum sample. For e.g. ,ovarian cancer
antigen (CA-125) enzyme immunoassay test kit is intended for use as a monitoring and
screening test for serum CA-125 level. An elevated serum CA-125 level can indicate
ovarian cancer and suggests the need for further clinical management, also determining
serum CA-125 concentration may be useful in monitoring patients with diagnosed ovarian
cancer.

Materials provided with the test kits includes antibody coated microtiter plate with 96 wells,
enzyme conjugate reagent, substrate solution, stop solution, wash buffer concentrate,
sample diluent, reference standards, positive and negative controls.
ELISA results are reported as a number and the most controversial aspect of this test is
determining the "cut-off" point between a positive and negative result. A cut-off point may
be determined by comparing the ELISA plate reader value with a known reference
standard. If an ELISA test is used for drug screening at workplace, a cut-off concentration,
50 ng/mL, for example, is established, and a sample will be prepared which contains the
standard concentration of analyte. Unknowns that generate a signal that is stronger than
the known sample are "positive" and those that generate weaker signal are "negative."
Materials and methods:

Materials:
• Multichannel pipette & tips
• 1 mL, 200 uL, and 20 uL pipette
• 96-well high-binding ELISA plate (Biofil.)
• Protein standard – Beta-lactoglobulin (Sigma)
• Milk protein extract (from Practical 9)
• Microplate reader (Bio-Rad.)
• Orbital shaker
• Buffers
§ Solubilisation buffer (1 x PBS (pH 7) containing 0.5% SDS and 2% beta
mercaptoethanol)
§ Blocking buffer – 1% soy protein isolates (SPI) dilute with 0.1 M NaCl (pH 11
adjusted to pH 7)
§ Washing buffer – PBST (1 x PBS (pH 7) containing 0.05% Tween 20)
• Detection Antibody - rabbit polyclonal anti- β- lactoglobulin antibody (Bethyl, UK)
• Secondary Antibody - goat anti- rabbit IgG-HRP conjugate (Abcam, UK)
• Substrate - 3,3',5,5'-Tetramethylbenzidine (TMB) (Thermo Fisher Scientific, USA)
• Stop solution – 1 M sulphuric acid (H2SO4)

Procedure:
Preparation of beta lactoglobulin standard (demonstrator’s part)
1. Dissolved 1.5 mg of beta lactoglobulin in 1.5 ml solubilisation buffer (1 mg/ml stock
solution). Vortex to mix well.
2. Prepared standards by performing a series of dilution (in solubilisation buffer):
1 mg/ml –(1:10)à 100 μg/ml –(1:10)à 10 μg/ml –(1:10)à 1 μg/ml—(1:10)à 100
ng/ml –(1:2)à 50 ng/ml –(1:2)à 25 ng/ml –(1:2)à 12.5 ng/ml –(1:2)à 6.25 ng/ml
–(1:2)à 3.13 ng/ml –(1:2)à 1.57 ng/ml
Indirect ELISA
3. Coat the 96-well plate with 100 μl beta lactoglobulin standards, milk extracts, and
solubilising buffer as blank (all in duplicates) at different dilutions in solubilisation
buffer. The plate was covered with parafilm and incubated at room temperature with
agitation at 250 rpm .
4. Discard solution in wells and wash wells 3 X with the washing buffer using squeezy
bottle.
5. Block wells with 200 μl blocking buffer and incubate plate at 37 °C with agitation/ at
room temperature for 1 h.
6. Discard blocking buffer and wash wells with washing buffer 3 X.
7. Add 100 μl of 1:5000 dilution of the detection antibody in 1 x PBS (pH 7) to wells and
incubate plate for 1 h.
8. Discard solution in wells and wash wells 5 X with washing buffer.
9. Add 100 μl of 1:15000 dilution of the secondary antibody in 1 x PBS (pH 7) to wells
and incubate plate for 1 h.
10. Discard solution in wells and wash wells 5 X with washing buffer.
11. Add 100 μl of TMB substrate to wells and incubate at RT for 15 min in the dark.
12. Stop the enzymatic reaction by adding 50 μl of 1 M sulphuric acid.
13. Measure the absorbance of standard and samples at 450 nm.

Quizzes
5. What is the mechanism of indirect ELISA? What makes the ELISA system
sensitive?
6. Why is it necessary to block unoccupied binding sites on the microtitre plates?
7. What can cause false positive in indirect ELISA? How do you overcome this
problem?
8. Discuss the limitations of indirect ELISA for the quantification of allergens.

Recommend improvements of the methods.

Practical 11: Rapid detection of mycotoxins from food samples using

immune biosensor (demonstration)
Learning outcomes:
1. To understand the principle behind biosensor as a rapid method in food diagnostics

2. To understand the component of biosensor
3. To apply biosensor in the detection of biological and chemical contaminants in food

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Rapid Methods in Food Analysis– A Practical Manual

DEPARTMENT OF FOOD SCIENCE

RAPID METHODS IN FOOD ANALYSIS

1 FST4201 | Faculty of Food Science and Technology, UPM

2 FST4201 | Faculty of Food Science and Technology, UPM

General Laboratory Safety Instruction

At the end of this laboratory session, students should be able to:

1. Understand the laboratory safety rules

Good Laboratory Practice includes the following:

3 FST4201 | Faculty of Food Science and Technology, UPM

4 FST4201 | Faculty of Food Science and Technology, UPM

• Place microscope glass slide in disinfectant

5 FST4201 | Faculty of Food Science and Technology, UPM

Guidelines for Report Preparation and Submission

2. Each report should contain the following:

5. Each group submits one report only.

6 FST4201 | Faculty of Food Science and Technology, UPM

Laboratory Report Assessments Rubric

Duplication of Missing the major

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8 FST4201 | Faculty of Food Science and Technology, UPM

Practical skills evaluation assessment criteria

Up to maximum of 1-5 % per indicator (to be evaluated in each practical session):

1. attendance at all laboratory sessions;

9 FST4201 | Faculty of Food Science and Technology, UPM

Psychomotor Assessments Rubric

10 FST4201 | Faculty of Food Science and Technology, UPM

Writing Lab Reports and Scientific Papers

11 FST4201 | Faculty of Food Science and Technology, UPM

Materials and Methods

12 FST4201 | Faculty of Food Science and Technology, UPM

How were they used?

13 FST4201 | Faculty of Food Science and Technology, UPM

General Comments on Style

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15 FST4201 | Faculty of Food Science and Technology, UPM

Practical 1 : Isolation of Vibrio parahaemolyticus using one-step and two-

V. parahaemolyticus is a major food-borne pathogen that causes worldwide health problems.

16 FST4201 | Faculty of Food Science and Technology, UPM

Typical colonial morphology on TCBS Agar is as follows:

Materials and Media:

17 FST4201 | Faculty of Food Science and Technology, UPM

1. Weigh 25 g of sample into a sterile stomacher bag.

1. Weigh 25g of sample into a sterile stomacher bag.

18 FST4201 | Faculty of Food Science and Technology, UPM

b) Streak enriched sample onto TCBS agar

19 FST4201 | Faculty of Food Science and Technology, UPM

Practical 2 : Isolation of Listeria monocytogenes using one-step

Foodborne listeriosis, caused by the pathogen L. monocytogenes, is a relatively rare but

20 FST4201 | Faculty of Food Science and Technology, UPM

throughout the world, it is hardly surprising that L. monocytogenes has become

Materials and Media:

21 FST4201 | Faculty of Food Science and Technology, UPM

7. Incubate the plates at 30°C for 48 h.

22 FST4201 | Faculty of Food Science and Technology, UPM

What is the purpose of each of the following media in this protocol?

23 FST4201 | Faculty of Food Science and Technology, UPM

Practical 3 : Isolation of Escherichia coli O157:H7 using one-step and two-

24 FST4201 | Faculty of Food Science and Technology, UPM

Materials and Media:

25 FST4201 | Faculty of Food Science and Technology, UPM

26 FST4201 | Faculty of Food Science and Technology, UPM

1. What is the purpose of each of the following media in this protocol?