Immunotechnology

Course content:

Lectures

Part I: Introduction to immunology

Chapter 1: Basic concepts in immunology

Overview of the immune system

The concept of an antigen and recognition structures

Self, non-self and clonal selection

Roles and properties of the immune system

Chapter 2: Structure and general organization of the immune system

Lymphoid organs: location, structure and function

Different immune cells: morphology, function and differentiation markers

Part II: Innate immunity and the inflammatory response

Chapter 1: Innate immunity

Innate immune cells and their receptors

Chapter 2: The complement system

Complement activation pathways

Effector pathways of the complement system

Regulation

Complement receptors

Complement and human diseases

Investigation of the complement system

Chapter 3: Natural killer (NK) lymphocytes

General characteristics of NK cells

Origin and maturation of NK cells

Functions of these cells

Mechanisms of recognition and NK-cell activation

NK-cell receptors

Involvement in antitumour immunity

Chapter 4: Neutrophils

Introduction to neutrophils

Origin and development of neutrophils: from the bone marrow to the inflammatory site

Neutrophil phenotypes and functional plasticity

Effector functions of neutrophils

Chapter 5: Inflammatory responses

Introduction

Different components involved in the inflammatory process

Different phases of inflammation

Different types of inflammation

Biological markers of inflammation

Treatment

Tutorials

Exercises on innate immune responses and inflammation

Exercises on the complement system

Scientific article analysis or presentations

Course content:

Lectures

Part I: Overview of metabolism

Chapter 1: Metabolic crossroads

Review of the different metabolic pathways

Chapter 2: Bioenergetics

Review of thermodynamics

Molecular mechanisms and electron transfer in the mitochondrial respiratory chain

Chapter 3: Enzyme catalysis

Enzyme structure and properties

Enzyme nomenclature and classification

Mechanism of enzyme action

Enzyme kinetics

Catalytic activity

Allosteric enzymes

Part II: Metabolism and regulatory processes

Chapter 1: Enzymatic and hormonal regulation

Enzymatic regulation

Hormonal and metabolic regulation

Chapter 2: Metabolism of carbohydrates and glycoconjugates

Glycolysis and its regulation

Regulation and disorders of glycogen metabolism

Signal transduction and membrane transport

Other pathways of carbohydrate metabolism

Chapter 3: Investigation of lipid metabolism

Organisation of lipid metabolism

Eicosanoid metabolism

Metabolism of fat-soluble vitamins

Regulation of lipid and fatty acid metabolism

Chapter 4: Amino acid metabolism

Amino acid biosynthesis

Catabolism of amino acid nitrogen and carbon skeletons

Conversion of amino acids into specialised products

Chapter 5: Integrative cell biochemistry

Free radicals and oxidative stress

Biochemistry of ageing

Nervous tissue metabolism and metabolic regulation of synapses

Module content:

Chapter I: Review of the molecular organisation of biomembranes

1. Biomembrane structure

1.1. Asymmetry of membrane lipid composition and distribution

1.2. Distribution of membrane proteins

2. Membrane fluidity

3. Targeting mechanisms

3.1. Intracellular vesicular trafficking of proteins

3.2. Post-translational protein modifications

3.2.1. Lipidation

3.2.2. Glycosylation

Chapter II: Membrane receptors and intracellular signalling molecules

Membrane receptors and their ligands

Receptor characteristics

Classification of receptors by location

1.2.1. Nuclear receptors

1.2.2. Membrane receptors

Types of membrane receptor

1.3.1. Ion-channel receptors

1.3.2. G protein-coupled receptors (GPCRs)

1.3.3. Receptors with intrinsic enzymatic activity

1.3.3.1. Receptor tyrosine kinases (RTKs)

1.3.3.2. Receptors with serine/threonine kinase activity

1.3.4. Receptors with guanylyl cyclase activity

1.3.5. Tyrosine kinase-associated receptors

1.3.6. Serine/threonine kinase-associated receptors

General scheme of a signalling pathway

Network of intracellular signalling molecules

Main adaptor proteins

Protein–protein interaction domains

3.1.1.1. SH domains (Src homology domains)

3.1.1.2. PTB domains (phosphotyrosine binding)

3.1.2. SH2-domain adaptor proteins

3.1.2.1. Grb2 protein

3.1.2.2. Shc protein

Small monomeric G proteins

3.2.1. Ras protein superfamily

3.3. Regulatory proteins associated with small G proteins

3.3.1. GTP/GDP exchange proteins (GEPs)

3.3.2. GTPase-activating proteins (GAPs)

3.4. Enzymes and intracellular second messengers

3.4.1. Properties of a second messenger

3.4.2. Second-messenger synthesis reactions and enzymes

3.4.2.1. Cyclic AMP and adenylyl cyclase

3.4.2.2. Diacylglycerol (DAG), inositol trisphosphate (IP3) and phospholipases C

3.4.2.3. Phosphatidylinositol bisphosphate (PIP2) and PI3-kinase; the source incorrectly pairs “trisphosphate” with PIP2

3.4.2.4. Cyclic GMP and guanylyl cyclase

3.5. Protein kinases

3.5.1. Phosphorylation reactions and kinase domains

3.5.2. Major protein kinases

3.5.2.1. Protein kinase A (PKA)

3.5.2.2. Protein kinase C (PKC)

3.5.2.3. Protein kinase B (Akt)

3.5.2.4. Mitogen-activated protein kinases (MAPKs)

Chapter III: Molecular basis of receptor tyrosine kinase signalling

Mechanisms of RTK activation

Receptor dimerisation

Receptor transphosphorylation

Activation of the mitogen-activated protein kinase cascade

MAPK-activated transcription factors: AP-1 (activator protein 1)

Activation of the phosphatidylinositol 3-kinase pathway

PI3K lipid kinase activity

PI3K classes

Class IA

Class IB

Roles of PI3K subunits

Mechanisms of PI3K activation by RTKs

Direct activation

Activation through the adaptor IRS-1 (insulin receptor substrate 1)

Activation by Ras

Recruitment of PDK1 (phosphoinositide-dependent kinase 1)

Activation of Akt (PKB)

Chapter IV: Signalling through G protein-coupled receptors

Heterotrimeric G proteins

G protein structure and subunits; subunit symbols are missing in the source

G proteins and subunit types s, i, q and 12; some symbols are missing in the source

G protein activation/inactivation cycle

Adenylyl cyclase activation by the G protein αs subunit

Phospholipase C activation by the G protein q subunit

4.1. Release of second messengers: DAG and inositol trisphosphate

4.2. DAG and protein kinase C activation

4.3. IP3 and intracellular calcium mobilisation

Contribution of a G protein subunit to PI3K activation; its symbol is missing in the source

CREB transcription factors

Chapter VI: Signal-dependent transcription factors

Simplified classification of transcription factors

Constitutively active transcription factors

Regulated transcription factors

Transcription factors regulated by a membrane signal

Nuclear factors (C/EBP and AP-1)

Cytoplasmic factors

STAT: signal transducer and activator of transcription

SMAD: Sma and Mad family

NF-κB: nuclear factor kappa B; the kappa symbol is missing in the source

Activation of STAT transcription factors by cytokine signalling

Definition and classes of cytokines

Receptors associated with cytoplasmic Janus tyrosine kinases (JAKs)

JAK family members

Receptor activation by JAK kinases

Signal transmission through STATs

STAT family members

STAT protein structure

STAT activation and translocation to the nucleus

JAK/STAT activation by IL-6

JAK/STAT activation by interferon; subtype not visible in the source

Activation of SMAD transcription factors by transforming growth factor; suffix not visible in the source

SMAD family members

SMAD protein structure

Canonical SMAD activation by serine/threonine kinase receptors

Canonical NF-κB activation by IL-1 and tumour necrosis factor; TNF suffix not visible in the source

4.1. NF-κB

4.1.1. NF-κB family members

4.1.2. Structural characteristics of NF-κB

4.1.3. IκB inhibitory proteins; subtype symbols missing in the source

4.1.4. IKK (IκB kinase)

4.2. NF-κB activation by IL-1

4.2.1. IL-1 receptor complex

4.2.2. MyD-dependent IL-1 signalling; the source symbol is truncated

4.3. NF-κB activation by TNF; suffix missing in the source

4.3.1. TNF receptors; suffix missing in the source

4.3.2. Signalling through the type 1 TNF receptor

4.4. NF-κB-responsive genes

Chapter V: Contributions of AI to the study of cellular signalling pathways

Protein interaction network analysis with STRING

How STRING works: data sources and confidence scores

Visualising a signalling network, such as MAPK

Interpreting connections: central proteins, hubs and complexes

Functional enrichment and pathway exploration with ShinyGO

Gene Ontology and pathways in KEGG and Reactome

Analysis of a gene/protein dataset

Identification of significantly enriched signalling pathways

Predicting 3D signalling-protein structures with AlphaFold

From sequence to structure: prediction principles

Using the AlphaFold Protein Structure Database

Identification of functional domains, such as kinase and SH2 domains

Practical case: visualising a key protein in PyMOL or ChimeraX

Integrated case study: the PI3K–AKT pathway

Network reconstruction with STRING

Enrichment of associated functions with ShinyGO

Visualising AKT or PI3K structure via AlphaFold

Discussion: combining tools to understand cellular regulation

Limitations, outlook and research opportunities

Data limitations and interpretation of results

Complementarity with experimental approaches

Course content:

Introduction to molecular biology

Definition

Historical background

The central dogma of molecular biology

Structure of nucleic acids

1. Chemical components of nucleic acids

1.1. Nitrogenous bases

1.2. Pentoses

1.3. The phosphate group

2. Nucleosides and nucleotides

2.1. The N-glycosidic bond and the resulting nucleosides

2.2. The phosphoester bond

2.3. The pyrophosphate bond

2.4. Nomenclature

3. Nucleotide polymerisation

3.1. Phosphodiester bonds and formation of nucleotide polymers

3.2. Notation conventions

4. Deoxyribonucleic acid (DNA)

4.1. DNA structure

4.2. Characteristics of the double helix

4.3. Physicochemical properties of DNA

4.4. Three-dimensional structure, compaction and higher-order organisation

5. Ribonucleic acids (RNA)

5.1. Structure and characteristics of ribonucleic acids

5.2. Types of ribonucleic acids: synthesis and function

6. Nucleic acid manipulation

Exonucleases and restriction endonucleases.

Genome and gene organisation

Definitions

Genome organisation

2.1. Genome content

2.2. Genome variability

2.3. Similarities between genomes

2.4. Prokaryotic genomes

Chromosomal DNA

Extrachromosomal DNA: plasmids

2.5. Eukaryotic genomes

Heterogeneity of DNA sequences

Highly repetitive DNA

Moderately repetitive DNA

Non-repetitive DNA

Mitochondrial DNA

2.6. Genome plasticity and transposable elements

Gene organisation

3.1. In prokaryotes

3.2. In eukaryotes

3.3. Types of genes

Single-copy genes; structural genes, regulatory genes, pseudogenes and housekeeping genes.

Gene families and superfamilies: homologues, paralogues, orthologues and xenologues

DNA replication

Overview

Fundamental principles of replication

2.1. Semiconservative replication

2.2. Origin of replication

2.3. Bidirectional replication

2.4. Unidirectional polymerisation

2.5. Semidiscontinuous replication

2.6. RNA primer

Replication enzymes

3.1. Helicases

3.2. Topoisomerases

3.3. Primase

3.4. DNA polymerases

3.5. DNA ligase

Replication proteins

Replication in prokaryotes

5.1. Proteins involved

5.2. Replication origins and termination in E. coli

5.3. Stages of prokaryotic replication

5.4. Regulation of replication in E. coli

Replication in eukaryotes

6.1. Eukaryotic DNA polymerases

6.2. Telomeres and telomerases

Histones and replication

Replication of retroviral genetic material

Variation and maintenance of genetic material

Introduction

DNA damage

Endogenous damage

Replication errors

Tautomerisation

Depurination and depyrimidination

Deamination

Methylation errors

Damage caused by exogenous agents

Damage caused by physical mutagens

Damage caused by chemical mutagens

Prevention

Cellular responses to DNA damage

DNA repair

Immediate repair

Repair during replication

Direct reversal by photolyases

Direct reversal by alkyltransferases

Secondary repair

Base excision repair (BER)

Nucleotide excision repair (NER)

Mismatch repair

Repair of breaks by recombination

The SOS response in E. coli

Defects in repair systems: selected examples

Genetic variation

Types of point mutations

Classification by the nature of the mutation

Substitution, deletion and insertion mutations

Classification by the consequence of the mutation

Missense, nonsense, silent and frameshift mutations

DNA transcription

Overview

The transcription unit

Template strand and coding strand

Transcription in prokaryotes

Initiation

Elongation

Termination

Rho-dependent termination

Rho-independent termination

Processing of primary transcripts

Transcription in eukaryotes

Distinctive features of eukaryotic transcription

Eukaryotic RNA polymerases

The protein complex required for transcription

Eukaryotic promoters

Initiation

Elongation

Termination

Post-transcriptional mRNA processing in eukaryotes

Capping

Polyadenylation

Splicing

Translation

The genetic code

Components of the translation machinery

2.1. Ribosomes: synthesis, structure and function

2.2. tRNA: structure and role; aminoacyl-tRNA synthetases

a) Structure of tRNAs and isoacceptor tRNAs

b) Amino acid loading onto tRNA

Stages of prokaryotic translation

3.1. Initiation

3.2. Elongation

a. Coupling reaction

b. Peptide bond formation and release of the first tRNA

c. Translocation

3.3. Termination

Distinctive features of eukaryotic translation

Post-translational modifications

A. Definitions and examples

B. Phosphorylation

C. Histone acetylation and methylation

D. p53 acetylation

Introduction to applications of artificial intelligence in molecular biology

Definition of AI and key concepts: algorithms, machine learning and deep learning

Introduction to biological databases: NCBI, Ensembl and UniProt

Introduction to BLAST, Clustal Omega and AlphaFold

Introduction to AI applications in DNA/RNA sequence analysis: multiple sequence alignment and secondary structure prediction

Introduction to computational and AI-based genome annotation tools, including DeepGene and GeneMark

AI for promoter and alternative splicing prediction

Protein structure modelling, active-site prediction and simulation of translation

Tutorials:

Tutorial 01: Structure of nucleic acids

Tutorial 02: Genome and gene organisation

Tutorial 03: DNA replication

Tutorial 04: Variation and maintenance of genetic material

Tutorial 05: DNA transcription

Tutorial 06: mRNA translation

Tutorial 07: AI applications in molecular biology

Introduction to biological databases, bioinformatics tools and AI: BLAST, Ensembl and AlphaFold

Classifying sequences by similarity

Using a simple AI-assisted alignment tool

Basic demonstration of a supervised learning algorithm, such as a decision tree for classifying mutations as benign or pathogenic

Predicting RNA and protein structures with online AI tools

Course content:

Course content

Workshop 1: Solution preparation

- Review of concentration expressions (molarity, molality, normality, dilution, etc.)

- Buffers (preparation, pKa, buffer selection, etc.)

- Basic laboratory handling: glassware, volumes and pipetting

Workshop 2: Protein precipitation methods

- Effect of pH (pI)

- Salt precipitation (salting-out)

- Solvent precipitation (ethanol)

Workshop 3: Protein quantification by spectrophotometric methods

- Lowry method

- Bradford method

Workshop 4: Size-exclusion chromatography

- Demonstration by separating coloured molecules (dextran blue / fluorescein)

- Application to protein purification

- Spectrophotometric analysis of collected fractions

Workshop 5: Ion-exchange chromatography

- Application to whey protein purification

- Spectrophotometric analysis of collected fractions

- Affinity chromatography (IMAC: theoretical teaching)

Workshop 6: Protein electrophoresis under denaturing conditions: SDS-PAGE

- Tricine-SDS-PAGE (peptide electrophoresis: theoretical teaching)

Course content:

Workshop 1: Introduction to pharmaceutical chemistry practical work, including safety measures and hygiene.

Workshop 2: Available chlorine titration; preparation of aqueous solutions and sodium hypochlorite solution; preparation of an antiseptic solution.

Workshop 3: Preparation and identification of salicylic acid.

Workshop 4: Synthesis and identification of aspirin.

Workshop 5: Extraction of essential oils.

Workshop 6: Introduction to pharmaceutical formulation: compounding medicines in a pharmacy, including capsules, syrups, suppositories and ointments.

Workshop 7: Preparation and identification of hyaluronic acid.

Module content:

Lectures

Chapter 1: History of animal experimentation

History of animal use in research.

Use of animals in different research fields.

Chapter 2: Regulatory and ethical aspects

Ethics of research involving animals

Chapter 3: Hygiene and health monitoring in an animal facility

Animal facility equipment and materials: description, use and maintenance

Prevention of risks associated with laboratory procedures

Chapter 4: Rodents (rats and mice)

Anatomy

Characteristics of rodents

Rodent social behaviour and adaptability

Environment: impact on animal welfare

Reproduction

Major diseases

Chapter 5: Lagomorphs

Anatomy

Behaviour

Husbandry and reproduction

Major diseases

Chapter 6: Other animal models used in scientific research

Chapter 7: Experimental techniques

Monitoring biological parameters and validating experiments

Techniques, methodology and procedures followed during the different stages

of animal experimentation:

Techniques for administering substances: subcutaneous, intramuscular, intravenous and intraperitoneal injections.

Oral administration (gavage).

Selection of technique, administration volumes and frequency.

Dissection

Techniques for collecting physiological data: blood, urine, faeces, organs and tissues; choice of technique, volume and frequency.

Pain in animals during experimentation.

Euthanasia.

Chapter 8: The animal model concept

Choosing an animal model for scientific research

Relevance of animal models and transgenesis

Limitations of animal models

Alternative methods: cellular models

Practical work

Session 1: Rats and mice; restraint, gavage and injections

Session 2: Sampling methods

Session 3: Dissection, location and collection of lymphoid organs

Session 4: Animal surgery

Session 5: Stages of histological investigation (preparation and staining of histological sections).

Course content:

Chapter 1: Separation and fractionation techniques

Membrane-based separation and concentration techniques.

Fractionation techniques

Precipitation techniques

Chapter 2: Chromatographic techniques

Definitions and general principles of chromatography.

Classification of chromatographic techniques

General description of chromatographic separation and the mechanisms involved

Other types of chromatography and selection of a chromatographic system.

Chapter 3: Electrophoretic techniques

Zone electrophoresis

Isoelectric focusing

Two-dimensional electrophoresis

Capillary electrophoresis

Immunoelectrophoresis

Membrane transfer techniques and molecular hybridisation: Southern, Northern and Western blotting, among others.

Chapter 4: Spectroscopy

Introduction to spectroscopic techniques.

UV–visible molecular absorption spectrophotometry

Atomic emission spectrometry

Atomic absorption spectrometry

Fluorimetry

Nuclear magnetic resonance (NMR).

Course content:

Unit 1: Tell us about yourself

Grammar: Tenses (present, past, future). Question forms (where, what, who, why, how much).

Vocabulary: words with more than one meaning.

Reading: Cell communication.

Speaking: students of ESSBO and ESG2E talking about each other.

Listening: A scientist speaking about their career.

Writing: Informal letter.

Unit 2: The way we live

Grammar: Present tenses: present simple, present continuous.

Vocabulary: At the laboratory.

Reading: Living in Oran.

Speaking: Share with us your experience about living on campus.

Listening: Student life at MIT.

Writing: Transition (linking words).

Unit 3: Biologist from the past

Grammar: Past tenses: past simple, past continuous.

Vocabulary: Time expressions.

Reading: The extraordinary history of Kitab al-Hayawan.

Speaking: Telling stories.

Listening: Rosalind Franklin and the discovery of DNA.

Writing: write a short story about your favourite scientist.

Unit 4: Let’s go shopping

Grammar: Much/Many, Some/Any.

Vocabulary: Grocery shop.

Reading: Medina Jdida market.

Speaking: Talking about shopping habits.

Listening: Organic Food Market.

Writing: Short essay writing about enzymes market.

Unit 5: What do you want to do?

Grammar: Verb patterns, Expressing intentions

Vocabulary: Have, go, come.

Reading: what a DNA polymerase can do

Speaking: what are your plans?

Listening: What does a biological engineer do?

Writing: a nascent enzyme talking about its future plans

Course content:

Lectures

Part I: Adaptive immunity

Chapter 1: The adaptive immune response

Dynamics of adaptive immunity

Cell-mediated immune responses

Humoral immune responses

Chapter 2: Dendritic cells

Origin and subtypes of dendritic cells

Dendritic cell recruitment

Antigen recognition and capture

Functional maturation and migration of dendritic cells

Lymphocyte activation by dendritic cells

Therapeutic targeting

CD40 signalling and cDC1 activation

Chapter 3: Macrophages

Macrophage ontogeny and diversity

Macrophage activation, polarization and functional plasticity

Effector and immunoregulatory roles of macrophages

Macrophages in disease and therapy

Chapter 4: T lymphocytes

Origin, differentiation and repertoire of T lymphocytes

Adaptive immunity: T-lymphocyte activation and polarization

Adaptive immunity: regulatory T lymphocytes and the concept of tolerance

Regulatory T lymphocytes and disease

Adaptive immunity: the cytotoxic CD8+ T-cell response

Chapter 5: B lymphocytes

Diversity and ontogeny

B lymphocytes: differentiation and activation

Immunodeficiencies associated with B-cell activation and antibody production

Immunological memory

Chapter 6: Immunoglobulins

General structure of an immunoglobulin molecule

Antigen–antibody interactions

Effector functions of antibodies

Chapter 7: The human major histocompatibility complex (HLA)

The HLA gene complex

The two classes of classical and non-classical HLA genes

Formation of MHC–peptide complexes

Recognition of cell-surface MHC molecules by T lymphocytes

Other HLA molecules and related molecules

HLA and autoimmune diseases

Chapter 8: Mucosal immunity

Organization of mucosa-associated lymphoid tissue (MALT)

Intestinal innate immune cells

Intestinal adaptive immunity

Tutorials

Exercises for each chapter

Scientific article analysis or presentations

Course content:

Lectures

Part I: Peptides and proteins: structures and main properties

Chapter 1: Peptides

Classification and nomenclature

Physical and chemical properties

Study of selected biologically important peptides

Chapter 2: Proteins

Three-dimensional conformation: secondary, tertiary and quaternary structures

Protein denaturation

Determinants of three-dimensional conformation

Chapter 3: Main properties of proteins

Solubility and molecular mass

Amphoteric character and osmotic pressure

Protein isolation, fractionation and purification

Chapter 4: Classification of proteins

Classification by molecular shape

Classification by solubility

Classification by composition

Chapter 5: Protein dynamics and structural evolution

Protein folding

Protein structure design

Protein dynamics and engineering

Part II: Polysaccharides and glycoproteins

Chapter 1: Polysaccharides

Polysaccharides composed solely of sugar residues

Glycosides with a non-sugar moiety

Chapter 2: Glycoproteins

Monosaccharide constituents

Proteoglycans

Peptidoglycans

Glycoproteins

Chapter 3: Glycoprotein biosynthesis

Importance of glycoproteins

Role of glycan groups

Glycotechnologies

Part III: Lipids and membranes

Chapter 1: Lipids

Classification of membrane lipids

Properties of lipid aggregates

Chapter 2: Biological membranes

Biological membranes and structural dynamics

Membrane assembly

Chapter 3: Lipophilic hormones

General introduction to hormones

Structures, biosynthesis and roles of lipophilic hormones

Nuclear receptor superfamily

Mechanisms of action

Part IV: Nucleotides and nucleic acids

Chapter 1: Nucleotides

Pentoses

Nitrogenous bases

Nucleosides and their mono-, di- and triphosphates

Chapter 2: Nucleic acids

Primary structure

Determination of nucleotide sequences

Double-helical DNA

Secondary structure of RNA

Physicochemical properties of nucleic acids

Chapter 3: Nucleic acid synthesis

Synthesis of purine ribonucleotides

Synthesis of pyrimidine ribonucleotides

Formation of deoxyribonucleotides

Nucleotide degradation

Biosynthesis of nucleotide coenzymes

Course content:

Lectures

Chapter 1: Introduction to immunogenetics: concepts and multiple applications

Chapter 2: Immunogenetics in health

Genetics of innate immunity, including pattern recognition receptors (PRRs) and killer-cell immunoglobulin-like receptors (KIRs)

HLA and its genes

Genetics of antigen presentation

T-cell receptors (TCRs) and their genes

B-cell receptors (BCRs) and their genes

Crosstalk between immunity and DNA, including DNA repair, NETosis and mitochondrial DNA

Chapter 3: Immunogenetics in disease

Transplantation immunogenetics

Immunogenetics of immunodeficiencies

Immunogenetics of infectious diseases

Immunogenetics of the antitumour response

Immunogenetics of autoimmune diseases

Immunogenetics of neurological and psychiatric diseases

Chapter 4: Achievements of immunogenetics: immunotherapy; I came, I saw, I conquered

Tutorials

Inflammasomes and their regulation

Complement and the complosome

Interferon-stimulated genes (ISGs) in health and disease

Fundamentals of HLA typing

Epigenetic regulation of CD4+ T-cell differentiation

Immunotherapy and variability in response: the contribution of genetics

Course content

Part 1: RNA interference

I/ History and fundamental mechanisms of RNA interference

1. History of RNA interference

2. Fundamental mechanisms of RNA interference

2.1. Small interfering RNAs (siRNAs)

2.1.1. Biosynthesis

2.1.2. Mechanism of action

2.2. MicroRNAs (miRNAs)

2.2.1. Biosynthesis

2.2.2. Mechanism of action

2.3. PIWI-interacting RNAs (piRNAs)

2.3.1. Biosynthesis

2.3.2. Mechanism of action

II/ Practical implications for siRNA design

1. Influence of the intrinsic properties of siRNA

2. Constraints imposed by the target transcript

III/ Significance of RNA interference

1. A tool for understanding gene function

2. A tool for numerous therapeutic applications

IV/ Constraints associated with transfection of short nucleic acid sequences

1. Stability of interfering RNAs

2. Biodistribution

Part 2: Regulation of gene expression

Regulation of transcription

Regulation of transcription in prokaryotes

What is an operon?

An inducible catabolic operon under negative and positive regulation: the E. coli lactose operon

A repressible anabolic operon: the E. coli tryptophan operon

Regulation by conversion of a repressor into an activator: the E. coli arabinose operon (araBAD)

Other examples of operons

Regulation of open-complex formation

Regulation of the transition to elongation

Regulation of transcription in eukaryotes

Regulation at the chromatin level

Histone acetylation and methylation

DNA methylation

Transcriptional regulatory elements

Classes of transcriptional regulators

How transcriptional activator proteins function

Transcriptional repressors

Enhancer and silencer regulatory sequences

Gene silencing and epigenetic regulation

Post-transcriptional regulation in eukaryotes

Alternative splicing

Regulation by small RNAs

Regulation of mRNA stability in eubacteria

Components involved in degradation

Exoribonucleases

Endoribonucleases

RNA pyrophosphohydrolase (RppH)

Mechanisms of mRNA degradation

The direct-access pathway

The 5′-end-dependent pathway

The 3′ exoribonucleolytic pathway

Mechanisms regulating mRNA stability

Regulation of RNase activity and concentration

Effects of translation

RNA-mediated interference

Influence of the mRNA sequence

Regulation of mRNA stability in eukaryotes

Components involved in degradation

Exoribonucleases acting at the 3′ end of mRNA

Exoribonucleases acting at the 5′ end of mRNA

Endoribonucleases

Degradation mechanisms

The major pathway

Alternative pathways

Mechanisms regulating mRNA stability

The Lsm1–7 complex

Regulation of deadenylation

Regulation of the decapping complex

Interfering RNAs: miRNAs, siRNAs and piRNAs

Regulation of translation

Introduction

Regulation of translation initiation in eubacteria

Regulation of access to the ribosome-binding site (RBS)

Regulation through mRNA secondary structures

Regulation of translation initiation in eukaryotes

Regulation through translation initiation factors

Phosphorylation of initiation factor eIF2

Phosphorylation of 4E-BP proteins and availability of initiation factor eIF4E

Inhibition of initiation by miRNAs

Regulation through the 5′- and 3′-untranslated regions (UTRs) in eukaryotes

Regulation through 5′-UTRs

Interaction between 3′- and 5′-UTRs

Regulation through the 3′-UTR

Alternative initiation pathways

Upstream open reading frames (uORFs)

Initiation through an internal ribosome entry site (IRES) sequence

Regulation during elongation or termination in eubacteria

Regulation during elongation or termination in eukaryotes

Post-translational regulation: degradation of intracellular proteins

Introduction

Chaperone proteins: chaperonins

Proteolytic enzymes

Protein ubiquitination

The proteasome

Lysosomal degradation

Autophagy

Part 3: Contribution of molecular biology to the study of genetic diversity

Basic concepts

Biodiversity

Genetic diversity

Measuring genetic diversity

Morphological markers

Protein markers: biochemical markers

DNA markers: molecular markers

Restriction fragment length polymorphism (RFLP)

Amplified fragment length polymorphism (AFLP)

Minisatellites

Microsatellites

Single-nucleotide polymorphisms (SNPs)

Mitochondrial DNA markers

Examples of applications

Part 4: Artificial intelligence and molecular biotechnology

Introduction to artificial intelligence models and the design of siRNAs and primers. Study of siDirect and RNAxs; siRNA design criteria and target-site accessibility.

Introduction to artificial intelligence models applied to gene regulation. Study of DeepSEA for prediction of chromatin features and noncoding-variant effects; distinction from direct prediction of gene expression.

AI-assisted molecular diagnosis.

Applications of AI in phylogenetics, genetic clustering and variant detection (SNPs).

Ethical perspectives and limitations of AI in molecular biology.

Tutorials:

Tutorial sheet 1: Regulation of gene expression in prokaryotes (1): the tryptophan and lactose operons

Tutorial sheet 2: Regulation of gene expression in prokaryotes (2): the arabinose and histidine operons

Tutorial sheet 3: Regulation of gene expression in eukaryotes (1): study of bdnf gene structure, expression and function

Tutorial sheet 4: Regulation of gene expression in eukaryotes (2): study of c-myc gene expression regulation and function

Tutorial sheet 5: AI analysis of biological sequences: predicting siRNA sequence efficacy, motif extraction and promoter recognition

Tutorial sheet 6: Using notebooks (Google Colab) for simple examples of machine learning in biology: sequence classification and variant clustering

Course content:

Workshop 1: Solution preparation

Workshop 2: Genomic DNA extraction

Workshop 3: Quality assessment of extracted DNA

Workshop 4: Amplification of the 16S rRNA gene and the bacterial strain's gene of interest

Workshop 5: Species-level identification of the bacterial strain and phylogenetic tree construction

Workshop 6: PCR-RFLP

Course content:

Workshop 1: Molecular biology databases

Workshop 2: Sequence-analysis tools

Pairwise and multiple alignment of biological sequences

Detection of motifs in biological sequences using bioinformatics tools

Reconstruction of phylogenetic trees

Workshop 3: Introduction to immunoinformatics and IMGT®, the international ImMunoGeneTics information system

Workshop 4: Databases of antibody sequences and structures

Workshop 5: B-cell and T-cell epitope databases

Workshop 6: Databases for allergy prediction

Workshop 7: Therapeutic monoclonal antibody databases and related projects

Course content:

Chapter 1: The prokaryotic cell: structure and metabolism

Introduction

Metabolic pathways

Pathways at the crossroads of central and secondary metabolism

Secondary-metabolite production phase

Chapter 2: Microorganisms of applied interest

Bacteria

Yeasts

Moulds

Chapter 3: Enzymes

Introduction

Sources of enzymes

Synthesis

Applications

Chapter 4: Bacteriocins and antimicrobial substances

History

Classification and nomenclature

Biosynthesis mechanisms and their regulation

Detection, quantification and purification methods

Mechanisms of action

Applications

Chapter 5: Bacterial toxins and mycotoxins

General concepts

Production and biosynthesis pathways

Applications

Chapter 6: Exopolysaccharides

General concepts

Production

Application

Chapter 7: Vitamins

General concepts

Production and biosynthesis pathways

Application

Chapter 8: Other bioactive molecules

Plant-derived bioactive molecules

Animal-derived bioactive molecules

Application

Chapter 9: Preliminary characterisation of bioactive substances

Effect of pH

Effect of temperature

Effect of enzymes

Effect of organic solvents

Effect of storage

Course content

Chapter 1: Introduction to endocrinology

The three major integrative systems and overall body homeostasis

Cellular communication systems

The four major hormone classes: chemical nature and synthesis

Mechanisms of hormone action

Chapter 2: The hypothalamic–pituitary axis

- The limbic system and neuroendocrine transducers

The pituitary gland and its relationships with the hypothalamus

Hypothalamic hormones

Anterior pituitary hormones

The posterior pituitary and its relationships with the hypothalamus

Chapter 3: Thyroid hormones and their metabolic effects

Functional anatomy

Hormone biosynthesis and secretion

Regulation of hormone secretion

Physiological roles of thyroid hormones

Pathophysiology

Chapter 4: The endocrine pancreas

Anatomy and histology

Insulin: physiology

Regulation of metabolism by insulin

Glucagon: secretion, mechanism of action and regulation of metabolism

Diabetes mellitus

Chapter 5: The adrenal glands

Adrenal cortex: structure and function

Adrenocortical hormones: physiology and roles in metabolic regulation

Adrenal medulla: physiology of adrenomedullary hormones and their roles in metabolic regulation

Chapter 6: Calciotropic hormones and calcium–phosphate homeostasis

Calcium and phosphate movements

Parathyroid hormone

Calcitonin

Vitamin D3: cholecalciferol

Chapter 7: The pineal gland

Location

Structure

Roles

Melatonin: chemical structure and biosynthesis

Other secretions

Chapter 8: Endocrinology of adipose tissue

White and brown adipose tissue

White adipose tissue hormones: mechanisms of action and roles in metabolic regulation

Chapter 9: Immunoendocrinology

Hormone receptors and their interactions with immune cells: modulation of the immune response.

Course content:

Unit 1: Tell me what’s it like

Grammar: What it's like to? Comparative and superlative adjectives in biology.

Vocabulary: Talking about modern life.

Reading: “A story of two bacteria belonging to the same genus” - beneficial/pathogenic bacteria.

Speaking: Comparing cellulases from different sources.

Listening: Brenda Lee, Tell me what it's like.

Writing: Describing a wetland.

Unit 2: Asking scientific questions

Grammar: Present perfect and past simple in scientific writing.

Vocabulary: Adverbs in experimental protocols (slowly, carefully…).

Reading: scientist interview.

Speaking: questionnaire for research.

Listening: an interview with an eminent biologist.

Writing: writing a research protocol.

Unit 3: Do and don’t in the science Lab

Grammar: Have to, got to, should, must.

Vocabulary: Science laboratory safety symbols and hazard signs.

Reading: What can biologist do to help protect our environment?

Speaking: Do I need to be good at math to excel in biology? One question, many answers.

Listening: Fire safety in the Lab.

Writing: Should biologists have good math skills? (Argument essay).

Unit 4: Inventions that changed the world

Grammar: Passive voice.

Vocabulary: past participle verbs used in scientific writing (grown, produced, cultivated, shown, made…).

Reading: Agriculture, an invention that changed the world.

Speaking: Passive voice battleship.

Listening: The molecular biology.

Writing: Writing a documentary film review.

Course content:

Chapter 1: Review of the antigen–antibody reaction and its applications

Chapter 2: Techniques without labels

Precipitation in liquid media: immunoprecipitation

Precipitation in gels: immunodiffusion

Immunochromatography

Affinity measurement by surface plasmon resonance

Agglutination reactions

Use of the cytotoxic activity of complement

Chapter 3: Labelled techniques

Types of labels

Immunoassay techniques

Enzyme-linked immunosorbent assay (ELISA)

Fluorescence-linked immunosorbent assay (FLISA)

Radioimmunoassay

Multiplex bead-based immunoassays

Immunoblotting / Western blotting

Immunofixation

Protein arrays

Flow cytometry

Immunocytology and immunohistology

Tissue microarrays

ELISpot

Chapter 4: Molecular biology techniques used in immunology

Amplification techniques

Clonality testing and repertoire analysis

DNA microarrays

Cell-based assays

Cytological study of immune cells

Immunophenotyping

Cell proliferation

Chapter 5: Application examples

Complement investigations

Immunoglobulin investigations

Detection and quantification of cytokines and their receptors

HLA investigations

Somatic hypermutation and chromosomal translocations

Immunohaematological applications

Course content:

Lectures

Part I: Biology and environment of cultured cells

Chapter 1: Introduction

Origins of cell culture

Methods of obtaining cells

Chapter 2: Cell adhesion

Methods for studying cell adhesion

Regulation of cell adhesion

Controlling the detachment of adherent cells

How can adhesion to a substrate alter cell behaviour?

Chapter 3: Non-genetic variability in cell cultures

Single cells and cell populations

Internally driven fluctuations

Externally driven fluctuations

Chapter 4: Dynamics of the cellular microenvironment

From the extracellular matrix to the microenvironment

Evolution of the microenvironment through cell–matrix communication

A distinctive dynamic: the tumour microenvironment

Chapter 5: Challenges of animal cell culture in bioreactors

Main stirred reactor types

Influence of the cellular environment

Cell culture on microcarriers

Online bioreactor analysis and control

Chapter 6: Good cell culture practice

Raw materials

Equipment

Environment: the cell culture laboratory

Chapter 7: Cell cryopreservation

Physicochemical aspects of crystal formation

Biophysical effects of ice formation

Biological effects of ice formation

Freezing conditions

Part II: Cell culture methodology

Cell systems: primary cultures, cell lines and stem cells

Cell proliferation: growth curves in culture

Cell transformation: immortalisation and tumour transformation

Culture medium and conditions: cell culture systems.

Protocol study: preservation of cell lines; introduction to five major cell-line categories; obtaining a cell line; reference banks; purchasing or establishing a cell line, with the final source phrase abbreviated.

Cell-line cryopreservation: nitrogen and safety; freezing and thawing

Contamination in cell-line cultures:

Main types of contamination

Detecting contamination

Preventing contamination

Equipment use and maintenance: procedures and good practice

Chapter 1: Viability, cytotoxicity and genotoxicity

Methods for studying cell viability

Quantifying dead cells through loss of plasma membrane integrity

Combined detection of dead and live cells

Cytotoxicity: specific study of different cell-death pathways

Methods for studying cell proliferation

Chapter 2: Contribution of flow cytometry to cell culture

Principle of flow cytometry

Different labelling methods

Interpreting results

Applications

Part III: Integrated systems and specialised cultures

Chapter 1: Cell systems

Primary culture

Cell lines and hybridomas

Stem cells

Cell banks

Chapter 2: Culture systems

Organ and explant culture

Cell culture

Organotypic culture

Chapter 3: Cell culture

Suspension cell culture

Adherent cell culture

Monolayer and three-dimensional culture

Chapter 4: Specialised cultures

Culture conditions

Culture media

Industrial-scale culture.

Practical classes

Introduction to cell culture: good hygiene and handling practice

Density-gradient separation and counting of peripheral blood mononuclear cells, PBMCs

Culture of adherent cells, including monocytes, and detachment from culture plates using trypsin and Accutase

Culture of human umbilical vein endothelial cells, HUVECs

Bioethics and biosafety concepts are addressed throughout practical classes.

Course content:

Lectures

Review of immune-system physiology

Chapter 1: Pathophysiology of hypersensitivity

General concepts concerning allergens

Type I hypersensitivity

Type II hypersensitivity

Type III hypersensitivity

Type IV hypersensitivity

Hypersensitivity V

Hypersensitivity VI

Hypersensitivity VII

Chapter 2: Pathophysiological mechanisms of autoimmunity

Introduction

The concept of immunological tolerance

Genetic basis of autoimmunity

Environmental triggers

Hypothesised mechanisms initiating autoimmunity

Mechanisms of tissue injury mediated by autoimmune effectors

Chapter 3: Pathophysiological mechanisms of abnormal lymphocyte proliferation

Lymphoproliferative diseases: the concept of clonality

Pathophysiological mechanisms of lymphoproliferative diseases

Selected data on three prototypes of lymphoproliferative disease

Chapter 4: Mechanisms of antitumour immune surveillance

Introduction

Cancer immunoediting

Chapter 5: General mechanisms of primary immunodeficiencies

Origins of primary immunodeficiencies

Pathophysiological mechanisms of primary immunodeficiencies

Complement deficiencies

Defects of the phagocytic system

Severe combined immunodeficiencies

B-cell deficiencies

T-cell deficiencies

Chapter 6: Mechanisms of alloreactivity and graft rejection

Definition

Alloantigens

The allogeneic response

Mechanisms of action and molecular targets of the main immunosuppressants

Chapter 7: Immunology of pregnancy

Introduction

Maternal–fetal interfaces

Maternal immune responses and stages of pregnancy

Protective mechanisms at the placental interface

Chapter 8: Cellular senescence

Definition

Cell-cycle arrest

Senescence as a driver of ageing

Mechanisms underlying cellular senescence

Characteristics of senescent cells

Tutorials

Analysis of recent articles

Course content

1. Foundations of genomics and proteomics

1.1. Overview of prokaryotic and eukaryotic genome organisation

1.2. Extrachromosomal DNA: bacterial plasmids, mitochondria and chloroplasts.

2. Genome mapping

2.1. Genetic and physical maps

2.2. Markers for genetic mapping

2.3. Methods and techniques used for genetic mapping

2.4. Physical mapping

2.5. Linkage analysis

2.6. Cytogenetic techniques

2.7. Fluorescence in situ hybridization (FISH) in genetic mapping

2.8. Somatic cell hybridization

2.9. Radiation hybrid maps

2.10. In situ hybridization

2.11. Comparative genetic mapping

3. Genome sequencing projects

3.1. The Human Genome Project

3.2. Microbial, plant and animal genome sequencing projects

3.3. Accessing and retrieving information about genome projects from the web

4. Comparative genomics

4.1. Identification and classification of organisms using molecular markers: 16S rRNA typing/sequencing and SNPs

4.2. Using genomes to understand eukaryotic evolution

4.3. Monitoring emerging diseases and designing new medicines

4.4. Determining gene locations within a genome sequence

5. Transcriptomics

5.1. Introduction

5.2. Data acquisition

5.2.1. Next-generation sequencing (NGS): RNA-seq and small RNA-seq

5.2.2. Microarrays

5.2.3. qPCR, RT-PCR and qRT-PCR

5.3. Data description

5.4. Transformation, normalization and filtering

5.5. Transcriptome data analysis

5.5.1. Differentially expressed genes

5.5.2. Co-expressed genes

5.6. Interpretation

5.7. Characterization of a gene set

6. Proteomics

6.1. Aims

6.2. Strategies and challenges in proteomics

6.3. Proteomic technologies: 2D-PAGE, isoelectric focusing, mass spectrometry, MALDI-TOF and the yeast two-hybrid system

6.4. Proteomic databases

7. Functional genomics and proteomics

7.1. Transcriptome analysis for gene identification and functional annotation

7.2. Contig assembly

7.3. Chromosome walking and chromosome characterization

7.4. Identification of functional genes in the genome

7.5. Gene function

7.6. Forward and reverse genetics

7.7. Protein–protein and protein–DNA interactions

7.8. Protein microarrays and functional proteomics

7.9. Biomedical and clinical applications of proteomics

7.10. Introduction to metabolomics, lipidomics, metagenomics and systems biology

8. Artificial intelligence applied to omics data

8.1. Introduction to artificial intelligence applied to omics data

Basic concepts: machine learning, deep learning and neural networks

General applications in biological sciences

8.2. AI in genomics

Prediction of genes and functional elements in the genome

Automatic sequence annotation and classification

Large-scale comparative genome analysis

8.3. AI in transcriptomics

Identification of differentially expressed genes using predictive models

Grouping expression profiles through unsupervised clustering

Detection of transcriptomic signatures associated with biological conditions: diseases, stress, etc.

8.4. AI in proteomics

Mass spectral analysis using neural networks

Prediction of protein structure and function

Recognition of protein motifs and interactions

Tutorials:

Tutorial 1: Applications of omics approaches

Activity type: Collaborative work – concept map

Article: How ‘omics technologies can drive plant engineering, ecosystem surveillance, human and animal health

Aim: Introduce omics approaches through a visual synthesis activity

Tool/activity: Concept map creation and literature research

Tutorial 2: Genome mapping

Article: A physical map of the papaya genome with integrated genetic map and genome sequence – Qingyi Yu et al., 2009

Aim: Understand the foundations of genetic and physical mapping

Tool/activity: Integration of the existing guided tutorial sheet: guided questions and interpretation of results

Tutorial 3: Transcriptomic analysis and lncRNAs

Article: Genome-wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep – Xu Feng et al., 2018

Aim: Introduction to functional transcriptomics and long non-coding RNAs

Tool/activity: Integration of the existing guided tutorial sheet: guided questions and interpretation of results

Tutorial 4: Functional analysis with ShinyGO and STRING

Article: Functional annotation and network analysis of differentially expressed genes in a model organism or tissue

Aim:

- Analyse a set of expressed genes using ShinyGO: GO/KEGG enrichment

- Explore protein interactions using STRING

Tool/activity: Integration of the existing guided tutorial sheet: guided questions and interpretation of results

Tutorial 5: Simplified multi-omics pipeline: an integrated case study

Study material: Simulated data or a supplied real article, for example a stress response in a plant or animal

Aim:

- Combine RNA-Seq, ShinyGO, STRING, AlphaFold and InterPro

- Develop a coherent biological interpretation

Tool/activity: Integration of the existing guided tutorial sheet: guided questions and interpretation of results

Tutorial 6: AI and machine learning for omics analysis

Article: AI-assisted prediction of gene–disease associations

Aim:

- Introduction to AI: clustering, gene networks and deep learning

- Use of platforms such as Orange or DeepGO

Tool/activity: Integration of the existing guided tutorial sheet: guided questions and interpretation of results

Course content

Workshop 1: Enzyme-linked immunosorbent assay (ELISA)

Workshop 2: Western blotting

Workshop 3: Monocyte phenotyping and interpretation of results using ImageJ

Workshop 4: Observation of macrophage extracellular traps (METs) and interpretation of results

Course content:

Workshop 1: Extraction and purification of secondary metabolites from medicinal plants

Workshop 2: Extraction and purification of chlorophyll

Workshop 3: Synthesis and characterisation of nanoparticles using a microbial support.

Workshop 4: Extraction and purification of an antimicrobial substance from a eukaryotic organism.

Workshop 5: Extraction and purification of exopolysaccharides from a microorganism.

Workshop 6: Extraction and purification of bioactive molecules from microalgae.

Course content:

Lectures

Part I: Fundamentals of pharmacology

Chapter 1: Pharmacodynamics

- Different molecular targets

- Different receptor families

- Interactions with regulatory systems

Chapter 2: Pharmacokinetics

- Definitions

- Pharmacokinetic stages

- Pharmacokinetic parameters

Part II: Basic concepts in molecular pharmacology

Chapter 1: Neurotransmitters

- Basic principles of neurotransmission

- Neurotransmission systems

Chapter 2: Prostaglandins and related derivatives

- Structure

- Biosynthesis and biotransformations

Chapter 3: Biological and anti-cytokine therapies

- Cytokines

- Biological agents for treating autoimmune diseases

- Efficacy and tolerability

Part III: Xenobiotic metabolism

Chapter 1: Enzyme induction

- Inducible enzymes and associated agents

- Mechanisms of enzyme induction

Chapter 2: Enzyme inhibition

- Fundamentals

- Transport inhibition

Part IV: Toxicology

Chapter 1: Cellular toxicity

Molecular targets

Cellular targets

Chapter 2: Genotoxicity

Immunotoxicity of xenobiotics

Organ-specific or systemic manifestations

Part V: Pharmacogenetics, pharmacogenomics and personalized therapy

Chapter 1: General introduction to personalized medicine

Clinical research and pharmacogenomics

Genetic testing and phenotyping

Advances in pharmacogenomics

Chapter 2: New approaches to personalized therapy and their applications

Tutorials: Experimental pharmacology

Methods of investigation in pharmacology

Experimental models

Potential targets of pharmacological agents

Implications of selected molecular concepts

Drug metabolism and therapeutic effects

Drug development: ligand–receptor interactions

Genetic polymorphisms

Role of biomarkers in different fields and in oncology

Course content

Introduction to programming

What is a program? Programming languages

Why choose Python for biology?

Examples of scientific applications

Installation and getting started

Installing Anaconda

First Python script

Running cells, saving and comments

Variables and data types

Primitive types: int, float, str, bool

Tuples, sets, lists and dictionaries

Mathematical and logical operators

Expressions and basic statements (input, output and assignment)

Control structures

Conditional statements: if, elif, else

Comparison operators

Repetition structures

for and while loops

break and continue statements

Iterating over lists

Functions

Defining a function with def

Parameters and return values

Files

7.1. Reading and writing .txt and .csv files

7.2. open(), read() and write() methods

Course content

Unit 1: The Wonder World

Grammar: auxiliary verbs (do, be, have), naming the tenses, questions and negatives, short answers.

Vocabulary: social expressions.

Reading: wonders of biology.

Speaking: Biology Quiz (using auxiliary verbs, questions and negatives and short answers).

Listening: Ten craziest things cells do.

Writing: Find the mistake and correct it.

Unit 2: Bioethics and biosecurity

Grammar: Present tense.

Vocabulary: Numbers in science.

Reading: Bioethics.

Speaking: Debate on ethics in bioengineering.

Listening: Biosecurity.

Writing: writing a paragraph to describe scientific facts using present tense and numbers.

Unit 3: Telling science stories

Grammar: Past tense.

Vocabulary: graphical representations.

Reading: Agro-industrial residues valorisation.

Speaking: Debate on environmental impacts of biomass.

Listening: Agro-industrial wastes valorisation.

Writing: writing a paragraph to describe methods and results.

Unit 4: Enzyme engineering

Grammar: Modal verbs.

Vocabulary: Enzyme engineering vocabulary

Reading: Can crop residues provide fuel for future transport?

Speaking: Promoting critical thinking with English modal verbs.

Listening: Can enzymes be reused?

Writing: writing a paragraph about the perspectives of enzymes applications using modal verbs.

Unit 5: The future of enzyme technology.

Grammar: future forms

Vocabulary: genetic engineering vocabulary

Reading: Future trends of biotechnology.

Speaking: What role do you think industrial biotechnology will play in the future?

Listening: The future of energy.

Writing: Write an email to your internship supervisor to explain what will your plan on arrival.

Course content:

Lectures

Chapter 1: Vaccine mechanisms of action and the role of adjuvants

History of vaccination

The classical post-vaccination immune response: neutralising antibodies

Types of vaccines

Routes of administration

The concept of adjuvants

Individual and collective protection

Current challenges in vaccination

Chapter 2: Phage mechanisms of action

History and discovery of bacteriophages

Principles of phage therapy

Chapter 3: Mechanisms of action of polyvalent immunoglobulins

Immunoregulatory mechanisms of polyvalent immunoglobulins

Chapter 4: Mechanisms of allergen-specific immunotherapy or allergen desensitisation

Principles and modalities of allergen-specific immunotherapy

Mechanisms of allergen-specific immunotherapy

Chapter 5: Roles and mechanisms of therapeutic antibodies and Fc fusion proteins

Immunogenicity of therapeutic antibodies

Therapeutic antibodies that neutralise soluble targets

Antagonistic therapeutic antibodies

Cytolytic therapeutic antibodies

Anti-TNF biological medicines

Chapter 6: Targets and mechanisms of cytokine therapies

Interferons

Interleukins

Chapter 7: Targets and mechanisms of immunosuppressants

Effects of immunosuppressants on the immune response

Classification of immunosuppressants

Therapeutic strategies in organ transplantation

Chapter 8: Mechanisms and immunological targets of glucocorticoids

Main mechanism of action

Non-genomic mechanisms of action

Therapeutic targets

Chapter 9: Targets and mechanisms of cellular immunotherapy approaches

Adoptive cellular immunotherapy associated with allogeneic haematopoietic transplantation

Autologous adoptive cellular immunotherapy

Adoptive cellular immunotherapy for autoimmune diseases

Active cellular immunotherapy: dendritic cells as a cellular vaccine

Chapter 10: Immunological aspects of gene therapy

Gene therapy

Immune responses

Tutorials

Gene and cell therapy; vaccine production; immunotherapy and serum therapy.

Cytokine production; systematic studies of expression and interactions.

Module content

Chapter 1: Nanomaterial–immune system interactions

- Properties of nanomaterials for biomedical use

Classification of nanomaterials: organic (liposomes and polymers) and inorganic (gold, silica and carbon)

Physicochemical properties: size, charge, shape and surface

Influence on absorption, distribution, metabolism and excretion (ADME)

- Immunotoxicity and immune recognition of nano-objects

Protein corona: adsorption and recognition by pattern-recognition receptors

Complement activation and cytokine release

Examples: toxicity of silver nanoparticles and titanium dioxide

- Surface engineering and immunomodulation

Nanomaterial functionalisation: PEGylation, antibodies and targeting ligands

Reduced immunogenicity and specific targeting (dendritic cells and macrophages)

Stealth versus immune-recognisable nanoparticles

Chapter 2: Nanotechnologies applied to immunotherapy

- Targeted delivery systems for immunomodulatory drugs

Encapsulation of immunoactive molecules: interleukins, antibodies and immunosuppressants

Stimuli-responsive nanoparticles (pH, enzymes and temperature)

Examples: nanoformulated curcumin and liposomal dexamethasone

- Nanovaccines and nanoparticulate adjuvants

Nanoparticles as vaccine platforms (mRNA, DNA and recombinant proteins)

Examples: lipid nanoparticles in COVID-19 vaccines (Pfizer/BioNTech and Moderna)

Adjuvants based on alumina, silica and polymers

- Tumour targeting and modulation of the immune response

Nanoparticles for delivery of immune checkpoint inhibitors (PD-1/PD-L1)

CAR-T immunotherapy and nanocarriers

Theranostics: combining therapy and imaging

Chapter 3: RNA, epigenetics and nanoimmunology

- Non-coding RNAs in immune regulation

MicroRNAs: roles in macrophage polarisation, lymphocyte activation and immune tolerance

Long non-coding RNAs: transcriptional regulation and interactions with chromatin

Examples: miR-155 as a pro-inflammatory activator and lncRNA NEAT1 in inflammasome regulation

- Epigenetics and immune system plasticity

Epigenetic mechanisms: DNA methylation, histone modifications and chromatin remodelling

Myeloid cells: epigenetic reprogramming by pathogens or nanomolecules

Innate immune memory (trained immunity) through sustained epigenetic changes in genome regulation

- Nanocarriers for epigenetic modulation and RNA delivery

Nanoparticles for targeted delivery of siRNA, miRNA and lncRNA

Epigenetic editing tools (e.g. CRISPR/dCas9 fused to epigenetic enzymes)

Emerging therapies: cancer (targeted delivery of tumour-suppressor miRNAs) and autoimmune diseases (inhibition of pro-inflammatory miRNAs using nanoparticles)

Chapter 4: Regulation, bioethics and emerging trends

- Safety, ethics and regulation of immunoactive nanomaterials

ISO standards and in vitro/in vivo testing

Risk assessment: biodistribution and long-term immunotoxicity

Social acceptance and transparency issues

- Nanoimmunology and the medicine of tomorrow

Immunonanodiagnostics: biosensors and magnetic nanoparticles

Personalised medicine: bioinformatics and prediction of immune responses

Outlook: cancer vaccines, immunoediting and combined nanotherapies

Practical work:

Practical 1: Modelling a nanoparticulate carrier for mRNA or siRNA

Objective: Introduction to designing an RNA carrier targeting an immune gene.

Practical 2: Production of silver nanoparticles by biosynthesis

Objective: Produce silver nanoparticles using a bacterial or plant extract.

Course content

Chapter 1: History of genetic engineering

Chapter 2: Enzymatic tools of genetic engineering

Restriction enzymes

The restriction phenomenon

Recognition sites

Isoschizomers

The restriction–modification system, RM

Origins of restriction enzymes

Restriction enzyme nomenclature

Types of cleavage produced by restriction enzymes

Classes of restriction enzymes

Methylation of restriction sites and inactivation of restriction enzymes

Uses of restriction enzymes

Other enzymes commonly used in genetic engineering

Polymerases

Ligases

Alkaline phosphatases

Nucleases

Other specific enzymes

Chapter 3: Molecular hybridisation

Review of the hybridisation reaction principle

DNA melting temperature

Factors affecting melting temperature

Molecular hybridisation

Liquid-phase hybridisation

Solid-support hybridisation

In situ hybridisation

Probes

Principles of nucleic acid hybridisation

The probe concept

Selected labelling strategies

Chapter 4: Vectors

General principles

Vector concept and properties

General principles of vector use

Plasmids

Using a plasmid

Plasmid preparation

Types of plasmids

Origin of replication

Bacteriophages

Uses of bacteriophages

Phage preparation

Phages used in molecular biology

Other types of vectors

Cosmids

Artificial chromosomes

Shuttle vectors

Eukaryotic viral vectors

Chapter 5: Cloning and recombinant protein expression

Cloning principles

PCR-based cloning

DNA libraries

Genomic DNA libraries

cDNA libraries

Expression systems

Choosing an expression system

Post-translational modifications

Prokaryotic expression systems

Recombinant protein expression cassettes

Characteristics of E. coli

Overview of heterologous protein expression in E. coli

Recombinant protein expression

Chapter 6: Genetically modified organisms, GMOs

Plant transgenesis

Plant transgenesis and conventional breeding

Plant transgenesis techniques

Transformation techniques

Animal transgenesis

Definition

Gene transfer methods in animals

Transgene construction

Other techniques for generating GMOs

Main applications of GMOs

GMO traceability and labelling

Chapter 7: New genetic engineering techniques and applications

Genome editing

Programmable nucleases

RNA interference

Zinc-finger nucleases

TALEN

CRISPR/Cas9

Course content

Chapter 1: Introduction to the immunology of infections

Definition and importance of the immune system in infectious diseases

Different pathogens and classification of infectious diseases

Chapter 2: Microbial pathogenesis

Stages of the infectious process

Host invasion and evasion of host defences by pathogenic bacteria

Damage caused to the host by pathogenic bacteria

Pathogenic properties of viruses

Pathogenic properties of fungi, protozoa, helminths and algae

Chapter 3: Pathogenicity and virulence factors

Adhesion and colonization factors: fimbriae, LPS, flagellum and secretion system

Invasion factors

Cytolytic factors

Toxins and superantigens

Chapter 4: Genetic basis of virulence

Virulence plasmid

Bacteriophage

Pathogenicity islands

Chapter 5: Immune responses by type of infection

2.1. Immunity to bacterial infections

2.2. Immunity to viral infections

2.3. Immunity to fungal infections

2.4. Immunity to parasitic infections

Chapter 6: Pathogen evasion mechanisms and resistance to immune defences

Antigenic modification

Inhibition of the immune response

Latency and reactivation of chronic infections

Chapter 7: Infection-associated immunopathology

Septic shock and cytokine storm

Post-infectious autoimmune diseases

Infection-associated hypersensitivity

Chapter 8: Therapeutic applications

Anti-infective immunotherapy

Immunomodulation

Module content:

Workshop 1: Production of lipopolysaccharide (LPS) from different bacterial strains

Session 1: Bacterial cell preparation and cell lysis

Session 2: Removal of protein and nucleic acid contaminants and hot phenol–water extraction

Session 3: LPS precipitation

Session 4: Recovery and final purification after dialysis

Session 5: LPS characterisation by SDS-PAGE

Session 6: Assessment of the mitogenic effect of LPS on immune cells such as monocytes

Separation of peripheral blood mononuclear cells (PBMCs) using Ficoll

Monocyte culture

Course content:

Techniques

Design cloning primers and simulate α-amylase gene cloning in silico with SnapGene.

Extract genomic DNA from the strain of interest.

PCR amplification for cloning using the cloning primers.

Purify the PCR product with a PCR Clean-up kit.

Digest the insert and plasmid vector, pET21/28 a+, with an appropriate restriction-enzyme pair.

Purify digestion products from agarose gel.

Ligate the gene into the plasmid vector.

Transform the cloning host E. coli DH5α.

Extract the genetic construct and transform the expression host E. coli BL21 (DE3).

Select transformed clones in the presence of an antibiotic.

Test recombinant enzyme expression by SDS-PAGE.

Purify the recombinant enzyme using a HisTrap affinity chromatography column.

Session 1, 05 hours:

Prepare solutions and culture media.

Design cloning primers.

Session 2, 06 hours:

Extract genomic DNA from a Bacillus sp. strain using a kit.

PCR amplification for cloning the gene of interest.

Simulate α-amylase gene cloning in silico using SnapGene.

Qualitative and quantitative tests: agarose gel electrophoresis.

Session 3, 06 hours:

Purify the PCR product and quantify DNA.

Digest the insert and pET21/28 a+ vector with the appropriate restriction-enzyme pair.

Sequencing simulation: in silico verification of the sequenced PCR product.

Electrophoresis of digestion products followed by agarose gel purification.

Session 4, 06 hours:

Prepare competent bacterial cells, part 01.

Ligate the gene into the plasmid vector.

Session 5, 06 hours:

Prepare competent bacterial cells, part 02.

Transform the cloning host E. coli DH5α.

Session 6, 08 hours:

Select transformed clones in the presence of an antibiotic.

Lecture on recombinant enzymes.

Extract the construct and transform the expression host E. coli BL21 (DE3).

Session 7, 06 hours:

Recombinant enzyme expression tests, part 01:

Prepare different cultures under different conditions.

Session 8, 06 hours:

Recombinant enzyme expression tests, part 02:

SDS-PAGE.

Session 9, 06 hours:

Purify the His-tagged recombinant enzyme using a HisTrap affinity column.

c) Course Content

I- Lectures

II- Practical Sessions:

Course content

1. Data manipulation with NumPy

Use NumPy arrays to represent biological data (sequences and matrices).

Apply vector operations and slicing to data analysis.

2. Biological data analysis with pandas

Read and manipulate CSV files (e.g. PCR results and enzyme assays).

Sort, filter and group data for experimental analysis.

3. Data visualisation with Matplotlib

Create plots (curves and histograms) to present biological results.

Customise visualisations (titles, legends and labels).

4. Object-oriented programming (OOP)

Fundamental concepts: understand classes, objects, attributes and methods; implement a simple class.

Inheritance and special methods.

5. Introduction to Biopython

Read and analyse FASTA files.

Extract information from DNA sequences (length and content).

Course content

Unit 1: The World of work

Grammar: Present perfect

Vocabulary: Work and employment vocabulary.

Reading: Dream jobs.

Speaking: What is your dream job?

Listening: Types of Biotech Companies.

Writing: Writing application letters.

Unit 2: Microalgae: the green gold of the future?

Grammar: Conditionals.

Everyday English: making suggestions.

Reading: High-added value products from microalgae.

Speaking: If you have funding, what would you do?

Listening: Biofuel from microalgae.

Writing: If the microalgae...

Unit 3: Food Biotechnology

Grammar: Reported speech.

Vocabulary: Vocabulary for biotechnology

Reading: Applications of enzymes in the Food Industry

Speaking: Is it safe to use enzymes in food?

Listening: Enzymes in milk & cheese.

Writing: Scientific text using reported speech.

Unit 4: Biofuel cell

Grammar: Expressions of quantity.

Vocabulary: Biofuel cells vocabulary.

Reading: Biofuel Cells, enzymes and microbes for energy production.

Speaking: Why don’t we have functional biofuel yet?

Listening: The future of bioenergy.

Writing: From excel to text, expressions of quantities.

Unit 5: Bioentrepreneurship

Grammar: Relative clauses.

Vocabulary: Entrepreneurship.

Reading: The three pillars of bioentrepreneurship.

Speaking: Biotechnology and economic development.

Listening: Biotechnology is the future of manufacturing.

Writing: scientific text using relative clauses.

Course content:

Part I: General introduction to oncogenesis

Chapter 1: Overview of oncogenesis

Mechanisms of oncogenesis

Oncogenes and tumour suppressor genes

Significance of mutations found in cancers and regulation of gene expression

Chapter 2: Malignant transformation

DNA alterations can induce malignant transformation

Discovery of oncogenes

Cancer progression: a multistep process

Part II: Antitumour immunity

Chapter 1: Antitumour immune responses: concepts and principal participants

Tumour antigens

Modelling the initiation of antitumour immune responses

Chapter 2: Regulation of T-cell activation

T-cell ontogeny and differentiation

Activation mechanisms and biological functions of T cells

Regulation of T-cell responses

Chapter 3: Role of B cells in antitumour immunotherapy

B cells: key participants in adaptive responses

Role of tumour-infiltrating B cells

Using B-cell properties to develop biotherapy strategies

Chapter 4: Roles of dendritic cells

Dendritic-cell activation and induction of immune responses

Dendritic cells in pathophysiological contexts

Immunotherapies targeting or using dendritic cells

Part III: Genomic and epigenomic alterations in cancer cells

Chapter 1: Ubiquitous cell-proliferation pathways

Receptor tyrosine kinases

MAP kinase pathway

PI3 kinase pathway

Chapter 2: Specialised proliferation pathways

Cytokine pathways and pathways involving G-protein-coupled receptors, GPCRs

Hippo or YAP/TAZ, purinergic and Wnt–β-catenin pathways

Notch and Hedgehog pathways, pathways leading to NFκB, and nuclear receptors

Chapter 3: Cell multiplication and death

Cell-cycle control

Control of apoptosis

Chapter 4: Adhesion and motility

Cell adhesion

Cell motility

Chapter 5: Cell-migration pathways

Chemokine, integrin and semaphorin pathways

Transforming growth factor beta, TGFβ, and ephrin pathways

Chapter 6: Transcriptional regulation

DNA methylation and post-translational histone modifications

Chromatin remodelling, alternative splicing and transcription factors

MicroRNAs and long non-coding RNAs

Chapter 7: Metabolism and intracytoplasmic regulation

Protein biosynthesis

Endoplasmic reticulum stress and autophagy

Protein ubiquitination and the proteasome

Part IV: From the cancer cell to cancer

Chapter 1: Genomic instability

Replication errors and mismatch repair

Endogenous oxidative processes and base excision repair

Single-strand breaks and nucleotide excision repair: distinct topics; their grouping does not imply that nucleotide excision repair repairs all single-strand breaks.

Double-strand breaks and repair by DNA recombination.

Chapter 2: Cell-line immortality

Telomeres

Telomerase

Alternative lengthening of telomeres, ALT

Chapter 3: Metastatic dissemination

Pathophysiology of metastasis

Genome and epigenome of metastasis

Epithelial–mesenchymal transition

Colonisation of target organs

Chapter 4: Angiogenesis

Stages of angiogenesis

Role of hypoxia

Angiogenic signalling

Chapter 5: Epithelial and non-epithelial cancers

Breast and colorectal cancers

Pancreatic cancers and hepatocellular carcinomas

Bladder, urinary tract and prostate cancers

Ovarian, cervical and endometrial cancers

Skin and thyroid cancers

Glioblastomas and soft-tissue sarcomas

Cutaneous melanomas

Leukaemias and malignant lymphomas

Chapter 6: Cancer immunotherapy

Monoclonal antibodies

Use of cytokines

Use of tumour-specific T cells expanded in vitro

Manipulation of costimulatory molecules

Tutorials

Document analysis and presentations on topics covered in lectures.

Course content

Part I: Normal microbiota in a balanced state

Chapter 1: Analysis and composition

Techniques for identifying and investigating the microbiota

Composition of the gut microbiota

Establishment and development of the microbiota

Factors modulating gut microbiota composition

Chapter 2: Gut microbiota and body functions

Host–microbiota dialogue

Microbiota and the barrier effect

Gut microbiota and the immune system

Gut microbiota and metabolic capacity

Part II: Microbiota in disease: dysbiosis

Chapter 1: Microbiota and digestive tract diseases

Infectious diarrhoea and antibiotic-associated diarrhoea

Microbiota and functional bowel disorders

Microbiota and coeliac disease

Chronic inflammatory bowel diseases

Role of the gut microbiota in short bowel syndrome

Ulcerative necrotizing enterocolitis

Microbiota and digestive cancers

Chapter 2: Microbiota and metabolic and liver diseases

Microbiota, obesity, dietary intake and bariatric surgery

Metabolic syndrome and diabetes

Microbiota and the liver: metabolic and nutritional liver diseases

Microbiota and enteral nutrition

Microbiota and childhood malnutrition

Chapter 3: Microbiota and other diseases

Microbiota and cardiovascular health

Microbiota and allergic reactions

Gut microbiota and psychiatric and neurodegenerative diseases

Microbiota and rheumatology/internal medicine

Gut microbiota and dermatology

Gut microbiota and gynaecology/urology

Microbiota and iatrogenic harm

Part III: Modulation of the gut microbiota

Chapter 1: Nutritional modulation

Early regulation

Short- and long-term regulation

Chapter 2: Probiotics, prebiotics and synbiotics

Definition

Regulatory frameworks

Classifications and properties

Current uses of probiotics

Mechanism of action

Chapter 3: Faecal microbiota transplantation

Definition and context

Regulatory frameworks

Transplantation

Faecal transplantation in the context of obesity

Faecal transplantation in the context of allergies

Chapter 4: Other approaches to modulation

Course content

Introduction: Welcome to R

Software installation

Basics of using R

Calculating means and standard deviations

Correlation and regression analysis

Graphical representations

Analysis of variance (one-way and two-way) and analysis of covariance

Statistical tests

Course content

Introduction to synthetic biology

Historical milestones

Definitions and aims of synthetic biology

The three major strategies: bottom-up, top-down and protocell approaches

BioBricks

DNA sequencing

DNA fabrication: basic building blocks

Natural and synthetic cellular chassis

Chemistry, biochemistry and recoding of living systems

Tools for controlling gene expression

Tools and approaches in synthetic biology

Engineering living systems and metabolic engineering

Synthia

Artemisinin synthesis

Bacterial systems used as environmental sensors and in biomedical diagnostics

Artificial genomes and the concept of xenobiology

Applications

Regulatory aspects and biosecurity

Safety, social and ethical aspects

Tutorials

Document analysis and preparation of presentations on topics covered in the lectures.

Module content

Session 1: Bacterial culture

Session 2: Heat inactivation

Sterility testing

Session 3: Preparation of PLGA microparticles

Session 4: Encapsulation of inactivated bacteria in PLGA microparticles

Session 5: Microparticle characterisation

Analysis of microparticle size and morphology.

Quantification of encapsulated proteins.

Session 6: Formulation with an adjuvant

Session 7: Immunisation of animal models

Selection and preparation of mice.

Subcutaneous or intramuscular injection of the formulation.

Session 8: Monitoring the immune response

Collection of blood samples.

Measurement of specific antibodies by ELISA.

Session 9: Challenge test

Exposure of immunised animals to the virulent bacterial strain.

Monitoring of clinical signs and mortality.

Session 10: Final analysis and storage

Compilation and analysis of immunological and protection data.

Course content:

Part I. Molecular docking

Chapter 1: Protein–ligand interactions

Protein–enzyme interactions

Protein–peptide interactions

Protein–protein interactions

Chapter 2: Identification of active sites

Chapter 3: Peptide design

Chapter 4: Application examples

Part II. Molecular dynamics

Course content:

Chapter 1: Introduction to pharmacognosy

Importance of natural substances in therapy.

Introduction to primary and secondary metabolites.

Chapter 2: Compounds of primary and secondary metabolism

Definition of the two types of metabolism.

Roles of primary and secondary metabolites, with plant examples.

Structural diversity of secondary metabolites.

Uses and applications of primary and secondary metabolites.

Chapter 3: Terpenes and steroids

Essential oils.

Resins, oleoresins, gum resins and balsams.

Iridoids.

Saponins.

Raw materials for the steroid industry.

Cardiotonic glycosides.

Chapter 4: Phenolic compounds

Phenolic compounds.

Phenols and phenolic acids.

Coumarins.

Lignans.

Flavonoids.

Anthocyanins.

Tannins.

Hydroxyanthracene derivatives.

Orcinols and phloroglucinols: Indian hemp.

Chapter 5: Alkaloids

General introduction to alkaloids.

Tropane alkaloids: belladonna, datura, henbane and coca.

Quinolizidine alkaloids: common broom.

Indole alkaloids: ergot of rye, rauwolfia, periwinkles and ochrosias.

Quinoline alkaloids: cinchonas.

Isoquinoline alkaloids: opium poppy.

Tropolone alkaloids: colchicum.

Alkaloids with an imidazole ring: jaborandi.

Diterpene alkaloids: aconite.

Purine bases: coffee, tea, kola and cocoa.

Chapter 6: Pharmaceutical formulation concepts

Main dosage forms in phytotherapy.

Practical application: extemporaneous preparations.

Criteria for selecting the dosage form.

Chapter 7: Phytotherapy and disease

Intrinsic plant toxicity.

Risks of medicinal plant–drug interactions.

Contraindications and precautions for medicinal plant use.

Chapter 8: Monographs

Different medicinal plants.

Indications for medicinal plants according to their properties in integrative clinical phytotherapy.

Chapter 9: Clinical and biological evaluation in choosing a medicinal-plant treatment and monitoring its effects

Phytopharmacology.

Clinical case studies.

Tutorials

Fundamental principles of phytotherapy, homeopathy and aromatherapy.

Dosage forms of herbal preparations.

Herbal pharmacovigilance and consumer safety.

Course content

Part 1:

Fundamental concepts of reverse engineering

Definition and history

Origins in mechanical and electronic engineering, followed by adaptation to the life sciences.

The importance of reverse engineering in modern biology: understanding, improving and reproducing.

Differences between reverse engineering and forward engineering

Forward engineering: a linear design process from idea to product.

Reverse engineering: starting with an existing product to infer its design.

Industrial applications

Maintenance and improvement of biological equipment, such as PCR instruments and sequencers.

Competitive innovation: bioprinting and developing alternative diagnostic tools.

Interoperability: compatibility between instruments, software and databases.

Technology Readiness Level (TRL) scale

Overview of the nine TRLs

TRL 1: Observation of basic scientific principles.

TRL 5: Technology validation in a relevant environment.

TRL 9: A system proven in an operational environment.

Positioning a biological project on the TRL scale

Examples: developing a rapid PCR test and producing experimental vaccines.

Resources needed to progress through the TRLs

Human, material and financial resources.

Planning pilot and pre-industrial trials.

Legal framework and intellectual property

The right to reverse engineer in relation to patents

Fair use, the Digital Millennium Copyright Act (DMCA) and European directives.

International comparative analysis

Managing legal risks

Drafting clear contracts, specific reverse-engineering clauses and anti-circumvention protections.

Legal limits

Reverse engineering permitted for analysis and interoperability; prohibited for unauthorised copying or resale.

Part 2: Applications in the biological sciences

1. Reverse engineering of biological systems

Biological deconstruction approach

Decomposing metabolic networks and signalling pathways.

Functional reconstruction from experimental data.

Practical examples

Oxidative stress response networks.

Molecular mechanisms of apoptosis.

2. Bioinformatics and free software in the biological sciences

Introduction to open-source software

Biopython, RStudio and Galaxy for biological analysis.

Practical workshops

Genome annotation with GenomeTools.

Analysing target-gene sequence data using FastQC and Clustal Omega.

3. Modelling and simulation in biology

Free simulation tools

COPASI for biochemical systems dynamics.

CellDesigner for modelling signalling networks.

Mini-projects

Simulating the dynamics of an inflammatory network.

Optimising a metabolic pathway using a dynamic model.

Part 3: Applications in immunotechnology. Students identify real examples of reverse engineering, use suitable open-source tools such as ImageJ, R/Bioconductor packages and FreeCAD, and reflect on ethical and legal implications.

Reverse engineering of antibodies and immunodiagnostics

Extracting and modelling three-dimensional antibody structures using RosettaAntibody and PyMOL.

Workshop

Reconstructing a rapid antigen test based on open-source antibodies.

Course content

Unit 1: Basic rules of language for scientific manuscripts

- Overview of language for scientific manuscripts

- Tenses

- Grammar

- Sentences

- Paragraphs

Unit 2: Common errors to avoid when writing a manuscript

Unit 3: Thesis defence

- What is a thesis defence?

- How to begin your presentation

- Formulating the research problem and objectives

- Describing the methods

- Describing and discussing the results

- Conclusions and future directions

- Working on transitions

- How to conclude your presentation

Unit 4: After graduation: what next?

- Identifying your career goals

- Preparing for a job interview

- Writing your CV

- Writing a cover letter

- Applying for a scholarship

Course content

Planning and conducting experiments

Based on the project proposal submitted in the previous semester, students should be able to plan and undertake an independent critical investigation as a final-year project in biotechnology. They should systematically identify relevant theories and concepts, relate them to appropriate methodologies and evidence, apply suitable techniques and draw appropriate conclusions. Students should work independently and understand the purpose and possible outcomes of each experiment they conduct.

Writing the dissertation

At the end of the project, students must write a dissertation covering all details, including the objective, methodology, results, discussion and future work. They may aim to publish their research findings in a peer-reviewed journal and may apply for a patent if the findings have application-oriented outcomes.