Semester 2 2022 / 2023

Pharmaceutical Biotechnology Year 3

Applied Biosciences and Biotechnology Year 3
BIOT7001 Applied Biotechnology
Mandatory 5 Credit Module
SPHBI_8_Y3 CRN 20202
SBIBI_7_Y3 CRN 15533

Delivered by: Dr. Rosemary Rea

Email: rosemary.rea@mtu.ie

BIOT7001 Applied Biotechnology Lecture 1 Slide 1

 Course Outline

Module Workload (Contact Time and Independent Learning)

• Class based – 4 hours a week

- Monday 16.00 – 17.00 IT2
- Tuesday 09.00 – 10:00 IT5
- Wednesday 13.00 – 14:00 IT5
- Thursday 13.00 – 14.00 T101

• Laboratory based – 4 hours a week

- Wed 14:00 – 18:00

• Self-directed study – 6 hours a week

BIOT7001 Applied Biotechnology Lecture 1 Slide 2

 Course Outline

Assessment Breakdown

• Course work – 100%

60% - Assessment
40% - Laboratory skills, techniques and written report / worksheets

BIOT7001 Applied Biotechnology Lecture 1 Slide 3

 Course Outline

Assessments
Week 1 – students notified of the week that assessments will
take place.

Applied Biotechnology Assessment schedule

Week 7 – Continuous assessment
Provisional Monday 07th March 60%

For assessment format and repeat requirements see

“BIOT7001 Applied Biotechnology Assessment Format” in the
Assessment unit in Canvas.

BIOT7001 Applied Biotechnology Lecture 1 Slide 4

 Course Outline
Missed Continuous Assessment

• Should a student have valid grounds for

missing an assessment he/she may be given
a maximum of one opportunity to take a
reassessment.

• The reassessment will take place at the

discretion of the Lecturer.

• The student will need to complete an

Individual Extenuating Circumstances
(IECs) claim form within 3 days of the
original assessment date.

• This will require the submission of

supporting evidence to your claim.

BIOT7001 Applied Biotechnology Lecture 1 Slide 5

 Course Outline
Grounds for Reassessment

• To be eligible for reassessment a student must meet certain criteria.

(a) Recent death of a parent/guardian, sibling, spouse or child.
(b) Recent death of a mother-in-law, father-in-law, grandparent/grandchild or any
person who was ordinarily resident in the home of the applicant.
(c) Debilitating illness.
(d) Circumstances outside the control of the applicant, which make it legally or
physically impossible for the student to attend the assessment.
(e) Wedding of an immediate family member if the wedding date coincides with the
assessment date.
(f) Other circumstances which the Lecturer considers to be analogous to any of the
above.

• Students must submit supporting evidence with application.

• Students should note carefully that if their application for

reassessment is unsuccessful the mark awarded for the original
assessment is zero.

BIOT7001 Applied Biotechnology Lecture 1 Slide 6

 Course Content
Protein Folding
Role of the protein quality control system - ubiquitin proteasome system and
chaperones. Protein misfolding and disease.

Drug Discovery and Development Process

High throughput screening in drug discovery. Lead compounds. Pre-clinical and clinical
trials. Drug approval processes.

Sources of Biopharmaceutical Proteins

Engineering of microbial and mammalian expression systems.

Biopharmaceutical Therapies
Monoclonal antibodies and other proteins. Vaccines. DNA based therapies.

Protein Engineering
An examination of the benefits of protein engineering using insulin as an example.

Laboratory Programme
Conduct relevant laboratory procedures and practical skills.

BIOT7001 Applied Biotechnology Lecture 1 Slide 7

 Lecture Plan (subject to change, if required)

• Week 1
- Monday Lecture 1 Introduction
- Tuesday Lecture 2 Protein Folding Diseases
- Wednesday Lecture 2 Protein Folding Diseases
- Thursday Lecture 3 Protein Folding Diseases
• Week 2
- Monday Research article review (Cystic Fibrosis Clinical Trials paper)
- Tuesday Lecture 4 Drug Discovery and Development
- Wednesday Lab prep
- Thursday Lecture 5 Drug Discovery and Development
• Week 3
- Tuesday Lecture 6 Herceptin and clinical trials paper review
- Wednesday Lab prep
- Thursday Lecture 7 E. coli expression system

• Week 4
- Monday Lecture 8 E. coli expression system
- Tuesday High throughout screening paper review
- Wednesday Lab prep
- Thursday Lecture 9 Lecture 8 Mammalian expression system (CHO)
• Week 5
- Monday Lecture 10 Monoclonal Antibodies
- Tuesday Lecture 11 Gene Therapy
- Wednesday Lab prep
- Thursday Lecture 12 Vaccines
• Week 6
- Monday Lecture 12 Vaccines
- Tuesday Lecture 13 Insulin and Protein Engineering
- Wednesday, Thursday Revision

BIOT7001 Applied Biotechnology Lecture 1 Slide 8

 Applied Biotechnology
Practical applications of biotechnology
• Pharmaceutical
- drug development
- prevent disease
- treat disease
- diagnostics
• Environmental
- waste treatment
- bioremediation
• Agricultural
- on the farm
- at the dinner table
• Food
- Beer, wine, cheese, yoghurt

BIOT7001 Applied Biotechnology Lecture 1 Slide 9

 Applied Biotechnology
Practical Application of Pharmaceutical Biotechnology

• Prevent disease – vaccines

• Treat disease
– antibiotics
– monoclonal antibodies
– gene therapy
• Diagnostics
– diagnose disease
– pregnancy test
– genetic testing

BIOT7001 Applied Biotechnology Lecture 1 Slide 10

 Applied Biotechnology
Practical Application of Pharmaceutical Biotechnology

• Prevent disease – vaccines

• Treat disease
– antibiotics
– monoclonal antibodies
– gene therapy
• Diagnostics
– diagnose disease
– pregnancy test
– genetic testing

BIOT7001 Applied Biotechnology Lecture 1 Slide 11

 Applied Biotechnology
Prevent Disease
Vaccines – biological preparations that generate an immune response,
thereby providing immunity.

Role of biotechnology
/ recombinant DNA
technology in vaccine
production?

BIOT7001 Applied Biotechnology Lecture 1 Slide 12

 Applied Biotechnology
Practical Application of Pharmaceutical Biotechnology

• Prevent disease – vaccines

• Treat disease
– antibiotics
– monoclonal antibodies
– gene therapy
• Diagnostics
– diagnose disease
– pregnancy test
– genetic testing

BIOT7001 Applied Biotechnology Lecture 1 Slide 13

 Applied Biotechnology
Treat Disease
Antibiotics
Monoclonal antibodies

Gene therapy

BIOT7001 Applied Biotechnology Lecture 1 Slide 14

 Applied Biotechnology
Practical Application of Pharmaceutical Biotechnology

• Prevent disease – vaccines

• Treat disease
– antibiotics
– monoclonal antibodies
– gene therapy
• Diagnostics
– diagnose disease
– pregnancy test
– genetic testing

BIOT7001 Applied Biotechnology Lecture 1 Slide 15

 Applied Biotechnology
Diagnose Disease
HIV test • Test serum diluted and applied to a plate
with attached HIV antigens
Positive HIV Test Negative HIV Test • If present HIV antibodies bind to the HIV
antigens.
• The plate is then washed to remove all
other components of the serum.
• A secondary antibody (that binds to
human antibodies) coupled to an
enzyme is added followed by another
wash.
• A substrate for the enzyme is applied,
and enzyme catalysis leads to a change
in colour or fluorescence.
• Confirmation of a positive test required.

BIOT7001 Applied Biotechnology Lecture 1 Slide 16

 Applied Biotechnology
Diagnose Disease
Cancer test
Detection and localization of surgically resectable cancers with a multi-
analyte blood test
Cohen et al. 2018
Science 18 Jan 2018 (Epub)
DOI: 10.1126/science.aar324
Abstract
Earlier detection is key to reducing cancer deaths. Here we describe a blood test
that can detect eight common cancer types through assessment of the levels of
circulating proteins and mutations in cell-free DNA. We applied this test, called
CancerSEEK, to 1,005 patients with non-metastatic, clinically detected cancers of
the ovary, liver, stomach, pancreas, esophagus, colorectum, lung, or breast.
CancerSEEK tests were positive in a median of 70% of the eight cancer types. The
sensitivities ranged from 69% to 98% for the detection of five cancer types (ovary,
liver, stomach, pancreas, and esophagus) for which there are no screening tests
available for average-risk individuals. The specificity of CancerSEEK was > 99%:
only 7 of 812 healthy controls scored positive. In addition, CancerSEEK localized
the cancer to a small number of anatomic sites in a median of 83% of the patients.

BIOT7001 Applied Biotechnology Lecture 1 Slide 17

 Applied Biotechnology
Diagnose Disease
CancerSEEK test
Their new test, which examines cancer-
related DNA and proteins in the blood,
yielded a positive result about 70% of the
time across eight common cancer types in
more than 1000 patients whose tumors had
not yet spread—among the best
performances yet for a universal cancer
blood test. It also narrowed down the form
of cancer, which previously published pan-
cancer blood tests have not.
The work, reported online today in Science,
could one day lead to a tool for routinely sc
reening people
and catching tumors before they cause
symptoms, when chances are best for a
cure.
BIOT7001 Applied Biotechnology
Examines the levels of 8
proteins and the presence of
mutations in 16 genes.
Among the best performances
yet for a universal cancer
blood test.
It also narrowed down the
form of cancer, which
previously published pan-
cancer blood tests have not.
Hope: could one day lead to a
tool for routinely screening
people and catching tumours
before they cause symptoms,
when chances are best for a
cure.
Lecture 1 Slide 18
 Applied Biotechnology
CancerSEEK test

Blood samples from 1005 patients with eight types of tumors that had evidently not yet
metastasized, the test detected between 33% and 98% of cases, depending on the
tumor type (see graph). The sensitivity was 69% or higher for ovarian, liver, stomach,
pancreatic, and esophageal cancers—all types that are difficult to detect early.
The test rarely found cancer that wasn't there. Only seven of 812, or less than 1%, of
healthy controls tested positive. And the test, called CancerSEEK, narrowed the origin
of the cancer to two possible sites in about 80% of patients.

BIOT7001 Applied Biotechnology Lecture 1 Slide 19

 Applied Biotechnology
Detection of COVID-19
PCR Based Serology Based
Antigen test

Antibody test

Alcoba-Florez. J,, González-Montelongo, R., Íñigo-Campos, A., García-Martínez de

Artola, D., Gil-Campesino, H., Ciuffreda, L., Valenzuela-Fernández, A. and Flores, C.
2020. Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab
samples. International Journal of Infectious Diseases, vol 97, 66-68.
https://doi.org/10.1016/j.ijid.2020.05.099.

Source: American Society for Microbiology

BIOT7001 Applied Biotechnology Lecture 1 Slide 20

 Applied Biotechnology
Diagnose Disease
How does it work?
HercepTestTM The biopsy sample is embedded in paraffin
wax and a thin slice is cut and attached to
a glass microscope slide.
An antibody that specifically recognizes
Her2 protein binds to the Her2 protein
molecules on the cancer sample on the
slide.
A second antibody that has a special
chemical attached, binds to the Her2
antibody.
Developing chemicals react with the
special chemical on the slide and cause a
brown dye to show where the Her2 protein
is in the cancer tissue sample.
The slide is then stained with a blue dye so
the doctor can see the other tissues.
A doctor that is trained to read the slides
uses a microscope to check the quality,
interprets the staining pattern, and reports
the results.
BIOT7001 Applied Biotechnology Lecture 1 Slide 21
 Applied Biotechnology
Diagnostics
Pregnancy test
Based on antibody –
antigen interaction
BIOT7001 Applied Biotechnology
Genetic testing
Newborn screening: just after birth to identify genetic
disorders that can be treated early in life. Diagnostic
testing: used to identify or rule out a specific genetic or
chromosomal condition.
Carrier testing: used to identify people who carry one
copy of a gene mutation that, when present in two
copies, causes a genetic disorder.
Prenatal testing: used to detect changes in a fetus's
genes or chromosomes before birth
Forensic testing: uses DNA sequences to identify an
individual for legal purposes.
Lecture 1 Slide 22
 Crop yield
Wastewater Disease resistance
Solid waste Biofertilisers
Gaseous waste Biopesticides
Bioremediation Nutrient enhancement
Pollution Biofuel

Agriculture

Environmental Plants
Genetic
Applied Engineering
Animals
Biotechnology Humans

Food Medicine

Fermentation
Beer Drugs
Wine Gene therapy
Cheese Diagnostics
yoghurt
BIOT7001 Applied Biotechnology Lecture 1 Slide 23
 Applied Biotechnology
TRADITIONAL BIOTECHNOLOGY

What is it?
- the use of natural organisms by humans to create or modify foods or other useful
products

Products
- breed food crops or domestic animals, food, beverages

MODERN BIOTECHNOLOGY

What is it?
- intentional manipulation of genes to generate changes in the genetic make-up of an
organism.

Products
- biopharmaceuticals

BIOT7001 Applied Biotechnology Lecture 1 Slide 24

 Applied Biotechnology
PHARMACEUTICAL (small molecule drugs)

What is it?
Any chemical substance intended for use in the medical diagnosis, cure, treatment, or
prevention of disease. Most traditional pharmaceuticals are low molecular weight
organic chemicals i.e. chemical synthesis
Products
- aspirin, antibiotics, acyclovir etc

BIOPHARMACEUTICAL (large molecule drugs)

What is it?
A protein or nucleic acid based pharmaceutical substance used for therapeutic or in
vivo diagnostic purposes, which is produced by means other than direct extraction
from a native (non-engineered) biological source
Products
- cytokines, growth factors, monoclonal antibodies, gene therapy etc

BIOT7001 Applied Biotechnology Lecture 1 Slide 25

 Applied Biotechnology

BIOT7001 Applied Biotechnology Lecture 1 Slide 26

 Comparison of Pharmaceuticals and
Biopharmaceuticals

Large molecule biologic Small molecule

biopharmaceutical pharmaceutical

Production Recombinant DNA Chemical synthesis

technology
Size High molecular weight Low molecular weight
Delivery Usually injected of infused Tablets etc
Intravenous and oral
Uniformity Heterogeneity Homogeneity
Off patent Biosimilar Generic

BIOT7001 Applied Biotechnology Lecture 1 Slide 27

 40% - Laboratory experiments and summary report and worksheets/activities

Aim of laboratory program:

• Flow 1: Identify potential antimicrobial producing soil isolates, crude
characterisation i.e. determine if peptide based
• Flow 2: Confirm identity of indicator microorganisms
• Generate a report for flow 1 and 2 – journal article style

• Referencing worksheet: 5% (completed in Canvas)

• Introduction overview: 3% (upload to Canvas)
• Electronic lab notebook: 10% (4 submissions, upload to Canvas)
• Report: 22% due 13th March (upload to Ouriginal and Canvas)

BIOT7001 Applied Biotechnology Lecture 1 Slide 28

 40% - Laboratory experiments and summary report / worksheet
Laboratory Plan

Week 2 01st February Understand the requirements for referencing and compete
referencing quiz
Prepare a serial dilution of a soil sample
Begin testing to confirm identity of indicator microorganisms
Update electronic lab notebook

Week 3 08th February Select soil isolates based on macroscopic morphology and
transfer to BHI agar for primary screening for antimicrobial
activity
Continue testing to confirm identity of indicator microorganisms
Update electronic lab notebook
Mind map and introduction list of contents to be uploaded
to Canvas for the following week

Week 4 15th February Overlay of soil isolates for primary screening for antimicrobial
activity
Confirmatory screening (well assay) for soil isolates identified
from a previous study
Update electronic lab notebook

Week 5 22nd February Read overlay and well assay results

Compile and organise report results
Update electronic lab notebook

Week 6 02nd March Reference Revision, Plagiarism and Results Recap

BIOT7001 Applied Biotechnology Lecture 1 Slide 29