Molecular Biology

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

Structure of tRNAs and isoacceptor tRNAs

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

Definitions and examples

Phosphorylation

Histone acetylation and methylation

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

Part 1: Microbial metabolism and microbial kinetics

Chapter 1: Culture media and exchange with the cell

Growth conditions

Substrate accessibility

Chapter 2: Kinetic study of microbial growth

Chemical balance

The biological phenomenon

Modelling

Chapter 3: Kinetic study of metabolite production

Chemical balance

The biochemical phenomenon

Modelling

Optimisation

Part 2: Bioengineering

Chapter 1: Microbiological basis of bioreactor design

Chapter 2: Transport phenomena in fermentation

Oxygen transfer

Bioreactor agitation

Agitator construction

Chapter 3: Bioreactor operating modes

Batch fermentation

Fed-batch fermentation

Continuous fermentation

Continuous fermentation with biomass recycling

Chapter 4: Types of bioreactors

Chapter 5: Fermentation facilities

Sterilisation and maintenance of aseptic conditions

Compressed-air distribution

Ancillary equipment

Process control and automation

Course content:

Extraction and purification of chromosomal and plasmid DNA

RNA extraction techniques

Electrophoresis and analysis of DNA digested with restriction enzymes

Bacterial transformation

PCR and its variants

Cloning and sequencing techniques

Southern blot, Northern blot, Western blot and dot blot

Molecular hybridisation

Course content

Chapter 1: Introduction to enzymology

Historical background

Definition

Structure

Enzyme properties and characteristics

Nature

Specificity

Efficiency

Compatibility with the environment and stability

Concentration

Location

Size

Nomenclature and classification

Nomenclature

Functional nomenclature

Official nomenclature

Classification

Oxidoreductases

Transferases

Hydrolases

Lyases

Isomerases

Ligases

Translocases

Chapter 2: Structure–function relationships

Functional structure

Isoenzymes

Active site

Binding site

Catalytic site

Active-site amino acids

Properties affecting enzyme–substrate binding

Models of enzyme–substrate binding

Forces involved in enzyme–substrate association

Chapter 3: The enzymatic reaction

Definition

Reaction mechanism

Factors

Enzyme

Substrate

Cofactor

Coenzyme

Factors affecting the enzymatic reaction

Physicochemical factors

Effectors

Substrate concentration

Enzyme concentration

Reaction time

Two-substrate enzyme reactions

Sequential mechanism

Double-displacement mechanism

Chapter 4: Enzymatic reaction energetics

Activation energy, Ea

Transition state

Enthalpy change, ΔH

Gibbs free energy change, ΔG

Spontaneity and reversibility

Chapter 5: Enzyme kinetics

Introduction to enzyme kinetics

Basic chemical kinetics

Phases of the enzymatic reaction

Initial-rate concept

Enzyme kinetics

Michaelis–Menten kinetics

Lineweaver–Burk linearisation

Chapter 7: Molecular mechanisms of enzyme catalysis

Proximity catalysis

Covalent catalysis

Acid–base catalysis

Metal-ion catalysis

Chapter 8: Enzyme inhibitors

Introduction to inhibition

Enzyme effectors

Inhibitor categories

Reversible inhibitors

Irreversible inhibitors

Applications of inhibitors

Inhibitor design

Chapter 9: Enzyme regulation

Definition of enzyme regulation

Regulatory enzymes

Regulatory processes

Allosteric regulation

Regulatory molecules

Covalent modification

Proteolytic cleavage/proteolysis

Regulation by isoenzymes

Genetic regulation

Course content

Introduction and explanation: review of laboratory safety.

Preparation of culture media for isolating lactic acid bacteria.

Isolation of lactic acid bacteria.

Preliminary identification of isolates by morphological characterization, catalase and oxidase tests, and amino acid catabolism studies: lysine and ornithine decarboxylases (LDC and ODC), arginine dihydrolase (ADH) and tryptophan deaminase; purification of isolates.

Screening for technological activities: proteolysis, lipolysis and caseinase activity, including measurement of casein degradation products by the Folin–Ciocalteu method; production of flavour compounds and exopolysaccharides (EPS); resistance to processing stresses involving acidic pH, salt, temperature and osmotic pressure; and selection of high-performing strains.

Identification of selected high-performing strains using API50CH strips and analysis of results with API-WEB.

Screening for biological activities: antimicrobial and antioxidant activity.

Strain preservation.

Cultivation in a fermenter.

Measurement of microbial culture growth parameters.

Kinetic study of lactic acid fermentation.

Assay of fermentation products.

Course content

Chapter I: Introduction and foundations

Fundamental concepts of secondary metabolism

Definitions and distinction between primary and secondary metabolism

Taxonomic distribution and biodiversity of secondary metabolites

Methodological approaches to secondary metabolite research

Evolutionary and ecological aspects

Evolutionary origins of secondary metabolism

General ecological roles

Intraspecific and interspecific interactions

Environmental adaptations

Chapter II: Secondary metabolites in plants

Major classes of plant secondary metabolites

Phenolic compounds and polyphenols

Phenolic acids, flavonoids, anthocyanins and tannins

Biosynthetic pathways and regulation

Terpenes and terpenoids

Classification, structures and properties

Mevalonate and methylerythritol phosphate pathways

Plant alkaloids

Structural diversity and classification

Biosynthesis from amino acids

Glycosides and other compounds

Biological functions in plants

Defence against herbivores and pathogens

Constitutive and inducible compounds

Direct and indirect defence mechanisms

Protection against abiotic stress

Communication and interactions

Intraplant signalling

Allelopathy and rhizosphere interactions

Attraction of pollinators and seed dispersers

Biotechnological applications of plant metabolites

Metabolic engineering for plant improvement

Production of pharmaceutically relevant metabolites

Agronomic and industrial applications

Biofortification and nutrition issues

Chapter III: Secondary metabolites in microorganisms

Diversity of microbial secondary metabolites

Fungal metabolites

Mycotoxins and bioactive compounds

Biotechnological applications

Bacterial metabolites

Antibiotics and antimicrobial compounds

Siderophores and signalling molecules

Metabolites of archaea and extremophiles

Secondary metabolites of microalgae

Chemical families of microbial metabolites

Polyketides: structures, PKS biosynthesis; erythromycin and aflatoxin examples

Nonribosomal peptides, NRPs: NRPS enzymatic mechanisms; bacitracin and surfactin examples

Microbial terpenoids: MVA/MEP biosynthesis; geosmin and carotenoids

Microbial alkaloids: cyanobacterial and actinomycete examples

Siderophores: catechol/hydroxamate structures and iron acquisition

Phenolic compounds: salicylic acid and protective pigments; phenazines listed here form a distinct chemical family and are not all phenols.

Bioactive pigments: prodigiosin, melanin and pyocyanin

Ecological roles and applications

Functions in microbial ecosystems

Intercellular communication and quorum sensing

Biofilm formation and maintenance

Interactions with plant and animal hosts

Pathogenicity and virulence

Symbiosis and mutualism

Industrial and environmental applications

Biorestoration and bioremediation

Biocontrol and agronomic applications

Production and manipulation techniques

Fermentation and production optimisation

Genetic engineering of microbial metabolic pathways

Synthetic and semisynthetic approaches

New metabolite-discovery strategies

Chapter IV: Secondary metabolites in humans and animals, within the programme’s broader scope

Introduction

Distinctive features of animal secondary metabolites

Comparison with plant and microbial metabolites

Biosynthetic origins and pathway evolution

Endogenous versus diet-derived metabolites

Horizontal gene transfer and symbiotic metabolism

Classification

Alkaloids

Distribution in marine and terrestrial species

Structural and functional characteristics

Phenolic compounds

Dietary antioxidants

Endogenous transformation and metabolism

Terpenoids

Steroids and steroid hormones; not all are secondary metabolites.

Pheromones and volatile signalling compounds

Glycosides

Bioactive derivatives and glycoconjugates

Physiological roles and applications

Secondary metabolite biosynthesis pathways

Terpene pathway

Steroid, hormone and pheromone synthesis

Hormonal and environmental regulation

Polyketide pathway

Bioactive compound production in marine species

PKS enzymes and multienzyme complexes

Nonribosomal peptides, NRPs

Animal toxins and venoms; distinguish ribosomal from nonribosomal origins rather than classifying all as NRPs.

Synthesis mechanisms and structural diversification

Amino-acid-derived pathways

Biogenic amine and neurotransmitter production

Neuropeptides and biological modulators

Origin and distribution

Dietary origin versus endogenous biosynthesis

Incorporation and transformation mechanisms

Detoxification and bioactivation

Taxonomic distribution

Vertebrates: amphibians, reptiles, birds and mammals

Invertebrates: insects, molluscs and echinoderms

Metabolites from microbial symbionts

Role of intestinal and tissue microbiomes

Host–microbiota metabolic interactions

Physiological functions and biological roles

Chemical defence

Venoms, toxins and repellents

Environmental adaptation and predation

Communication

Pheromones and chemical signalling

Social and behavioural mediators

Metabolic regulation

Homeostasis and physiological adaptation

Endocrine and neurological control

Protective functions

Antioxidant properties

Immune and antimicrobial functions

Extraction, analysis and investigation methods

Therapeutic and nutritional applications

Perspectives, challenges and current research

Chapter V: Secondary metabolism in yeasts and fungi

Diversity of fungal and yeast secondary metabolites

Mycotoxins: aflatoxins and ochratoxins

Fungal antibiotics: penicillin

Pigments: melanins and carotenoids

Ecological functions and biological interactions

Ecological competition

Mutualistic or pathogenic interactions

Biotechnological and industrial applications of relevant compounds

Practical classes

Screening, identification and extraction of secondary metabolites.

Quantification of secondary metabolites.

Purification: filtration, centrifugation, chromatography and electrophoresis.

Preservation: cold/cryopreservation, evaporation and freeze-drying.

Course content

Part 1: Literature Searching and Scientific Writing

Introduction to scientific research

Types of documents and scientific literature

Evolution of research methods

Open science and open access

Research methodology: advanced approaches

Defining the study question using PICO and 3QPOC

Selecting search tools: catalogues and multidisciplinary and specialist databases

Using specialist search engines and full-text platforms

Optimising and using search results

Assessing the relevance of sources

Reliability, currency and accuracy of information

Reference management and bibliographic software, including EndNote, Zotero and Mendeley

Modern scientific writing

Analysing papers and preparing reports

Writing a final-year dissertation

Writing scientific papers and conference contributions

Part 2: Scientific Communication and Knowledge Dissemination

Issues and purposes of scientific communication

Why and how should science be communicated?

Modern strategies and techniques for written and oral expression

Scientific interactions and exchanges in academic settings

How scientific exchanges work

Presenting and promoting research

Using digital tools to improve visibility

Open science and public science communication

Strategies for reaching the general public

Use of digital media and new technologies

Interaction with the press and media

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: Listening to a scientist speaking about his/her 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 popular market.

Speaking: Talking about shopping habits.

Listening: Organic Food Market.

Writing: Short essay writing about biomolecules 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 molecular biology enzyme talking about its function

Course content

Part 1: RNA interference

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

Practical implications for siRNA design

1. Influence of the intrinsic properties of siRNA

2. Constraints imposed by the target transcript

Significance of RNA interference

1. A tool for understanding gene function

2. A tool for numerous therapeutic applications

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:

Introduction: diversity and origins of the microbial world

The phylogenetic tree of life

Definition

The three domains: Bacteria, Archaea and Eukaryotes

The last universal common ancestor, LUCA

Phylogenetic approaches based on 16S/18S rRNA sequences

Types of phylogenetic trees

Morphological, metabolic and genetic diversity of microorganisms

Prokaryotes versus eukaryotes

Viruses

Part 1: Bacteria

Review of bacterial structure

Permanent components

Optional components

Chapter 1: Bacterial genome

Genome structure

Bacterial chromosome

Mobile genetic elements

Plasmids

- General plasmid organisation

- Plasmid classification

- Plasmid properties

1.2.2. Transposons

- General structure

- Types of transposons

- Bacterial transposition mechanisms

Replicative transposition

Conservative transposition

c. Effects of transposition on bacterial genome expression

1.2.3. Integrons

- Definition

- Integron structure

- Gene cassette structure

- Cassette movement

- Cassette expression

- Nature of cassettes

- Integron origins

1.2.4. Bacteriophages

Definition

Main characteristics

Mechanisms: lytic cycle, lysogenic cycle and lysogenic conversion

Prokaryotic gene organisation

Chapter 2: Horizontal gene transfer

Transformation

Conjugation

Transduction

Genetic maps

Part 2: Fungi, with yeast as a model system

Review of yeast biology

General principles

Culture and nutrition

Yeast genome

Yeast transcriptome

Yeast proteome

Tetrad analysis of biochemical mutations

Complementation and gene conversion

Mitochondrial genetics

Part 3: Archaea

Review of archaea

General principles

Archaeal diversity, ecology and evolution

Archaeal genetics

Asgard archaea

Part 4: Viruses

Chapter 1: Introduction to virology

Chapter 2: Molecular virology

Virion structure and composition

Viral infection cycle in a cell

Representative cycles: DNA viruses, RNA viruses and retroviruses

Virus–host interactions: cellular transformation, latency, antigenic variation, cancer, oncogenes and AIDS

5. Vaccination and antiviral agents

6. Handling and uses of viruses

7. Unconventional agents and prions

Chapter 3: Viral genetic variability

1. Mechanisms: mutation, recombination and reassortment

2. Dynamics of viral population evolution

3. Factors driving viral population evolution

Chapter 4: Biological consequences of viral population evolution

1. Antigenic variation and evasion of vaccine-induced responses

2. Antiviral treatment resistance

3. Host adaptation, interspecies transmission and viral emergence

4. Changes in viral tropism and pathogenesis

Chapter 5: Molecular modelling of viruses and viral protein structure–function relationships

Viral structures and molecular assemblies

Dynamic evolution and functional relationships of viral protein structures: envelope glycoproteins, proteases and polymerases

Applications to antiviral and viral vaccine design

Course content

Part 1: In vitro biology

Cell models and in vitro experiments

1.1. Introduction to cell biology and experimental approaches

Definition and objectives of cell biology

Emergence and objectives of cell culture

Defining in vitro, in vivo and in silico approaches

Cell systems

Primary culture of isolated cells

Tissue origin and collection

Enzymatic and mechanical isolation methods

Cell-line culture

Line types: immortalised and cancer-derived

Advantages and limitations of primary cultures versus cell lines

Criteria for selecting a cell system

Recent 3D cultures

Three-dimensional models: spheroids, organoids, organ-on-chip systems and 3D printing

Advantages and limitations compared with 2D cultures

Cell culture conditions

Culture types

Suspension culture: principles and applications

Adherent culture: principles and applications

Culture facilities and equipment

Biological safety cabinets: functions and importance; correction of the source’s inaccurate expansion of the French acronym PSM.

Incubators: temperature, humidity and CO₂

Microscopes and monitoring equipment: observing and controlling cell growth

1.3.3. Culture media

Media composition: basal medium, growth factors, serum and antibiotics

Adjusting pH, temperature and other specific parameters

Good laboratory practice

Contamination prevention and risk management

Biological waste management: safety and disposal protocols

Cell cryopreservation and thawing

Cell cryopreservation and freezing techniques

Freezing protocol and cryoprotectants such as DMSO

Cell recovery and post-freezing quality checks

Methods for studying cellular mechanisms

Basic analytical techniques

Flow cytometry

Immunofluorescence and immunohistochemistry

Electron, fluorescence and confocal microscopy, etc.

Studying cell proliferation

Cell growth-curve analysis

Proliferation markers: Ki-67, EdU and BrdU

Classical and recent methods: MTT, CCK-8 and high-throughput screening

Studying cell viability and death

Membrane-integrity testing with trypan blue; MTT measures metabolic activity rather than membrane permeability directly.

Apoptosis markers: Annexin V, caspases and TUNEL

Cell differentiation: models and specific markers

Integrating in vitro approaches into biomedical research

Models for high-throughput therapeutic compound screening

Studying signalling pathways in disease

Role of in vitro approaches in personalised medicine

Limits of extrapolating in vitro results to in vivo systems

Part 2: In vivo biology

Introduction to animal experimentation in biomedical research

Importance of animal models in scientific research

Ethics of animal experimentation

Criteria for selecting an animal model

Mouse models and genetic manipulation

Mouse embryonic stem cells

- Blastocyst origin

- Culture and characteristics

- Use in disease modelling and cell therapy

Genetic manipulation techniques

- Transgenesis: pronuclear injection and gene transfer into mouse embryonic stem cells

- Somatic cloning and nuclear transfer

- Gene knockout and knock-in: Cre/loxP and CRISPR/Cas9 systems

Mice in biomedical research

- Modelling cancer, neurodegenerative and infectious diseases, etc.

- Genetic advantages, reproducibility and available tools

Contributions of the rat, Rattus norvegicus

- Complementing mouse models in behavioural and metabolic studies

Drosophila as a model for stem cells and human diseases

Transition from mammalian models

Obtaining mouse embryonic stem cells and induced pluripotent stem cells, iPS cells

Limitations of mammalian models

Ethical considerations and limits of mammalian stem-cell use

Value of Drosophila in stem-cell biology

Drosophila stem cells

3.2.1. Germline stem cells in ovaries and testes

3.2.2. Intestinal stem cells

3.2.3. Other tissues: brain, follicles, etc.

3.2.4. Experimental advantages

Stem-cell regulation mechanisms

3.3.1. Niche and microenvironment roles

3.3.2. Conserved signalling: Notch, JAK/STAT, BMP and Wnt

3.3.3. Transcriptional control and epigenetic regulation

Reprogramming and cellular plasticity

3.4.1. Dedifferentiation and cell-state transitions

3.4.2. Modelling processes analogous to induced pluripotency

Human disease modelling

3.5.1. Neurodegenerative diseases: Parkinson’s, Alzheimer’s, etc.

3.5.2. Cancer and stem-cell dysregulation

3.5.3. Genetic screening and therapeutic target identification

Caenorhabditis elegans: a simple model for complex human diseases

Introduction to C. elegans

Biological characteristics

Experimental advantages

Conservation of fundamental molecular pathways

Studying ageing and longevity

Physiological ageing models

Genetic longevity pathways

Pharmacological screens

Metabolic and immune disorders

Insulin resistance models

Innate immune responses

Therapeutic compound screening

Limitations and ethical considerations

Favourable ethical aspects

Model limitations

Avian embryos as models in neurobiology and paediatric oncology

Introduction to the avian model

General characteristics of the chicken embryo, Gallus gallus

In ovo access to embryonic development

Experimental advantages: manipulation, visualisation and ethical considerations

Neuroblastoma: disease overview

Neuroblastoma origins in neural crest cells

Clinical features: paediatric tumour, heterogeneity and metastasis

Modelling neuroblastoma in avian embryos

Using the chorioallantoic membrane, CAM, for tumour-cell grafts

Studying invasion, angiogenesis and metastatic dissemination

In vivo visualisation and tumour-cell monitoring

Experimental and preclinical applications

Anticancer compound screening on the CAM

Limitations, perspectives and complementarity

Zebrafish as a model of melanoma and other human diseases

General introduction

Introducing the zebrafish model

Technical and experimental advantages

Biomedical and genetic relevance

Melanoma overview

Melanoma origin and progression

Main mutations: BRAF, NRAS, etc.

Diagnostic and treatment challenges

Studying melanoma in zebrafish

Generating transgenic models

Visualising tumour progression in vivo

Anticancer pharmacological screening tools

Xenograft approaches and immunosurveillance

Other diseases studied in zebrafish

Neurological disorders: epilepsy and autism

Cardiovascular diseases: cardiotoxicity and arrhythmias

Ethical issues in stem-cell research

Moral status of embryos

Trafficking in organs from aborted fetuses: an ethical/legal issue in the programme, not a description of legitimate research practice.

Exploitation of women

Stem-cell research policies

Laws and regulatory frameworks

Role of politics and public opinion

Influence on research policymaking.

Course content

Chapter 1: Amino acid structure/classification, peptides and the peptide bond

Amino acid structure

1.1. General structure: amino group, carboxyl group and side chain R.

1.2. Polar, nonpolar, acidic, basic, aromatic and other classes.

Peptides

2.1. Peptide formation through peptide bonds.

2.2. Peptides versus proteins.

Peptide bond

3.1. Condensation between one amino acid’s carboxyl group and another’s amino group.

3.2. Rigidity, planarity and polarity.

Chapter 2: Structural basis of proteins

Levels of organisation

1.1. Primary structure: linear amino acid sequence linked by peptide bonds.

1.2. Secondary structure: local regular α-helices, β-sheets and turns.

1.3. Tertiary structure: three-dimensional folding stabilised by noncovalent hydrophobic/ionic interactions and, where present, covalent disulfide bridges; the source incorrectly groups disulfides with noncovalent interactions.

1.4. Quaternary structure: assembly of subunits into a functional protein, e.g. haemoglobin; the ribosomal complex cited in the source is a ribonucleoprotein assembly, not exclusively protein.

Structural stabilising forces

2.1. Hydrogen bonds

2.2. Hydrophobic interactions and disulfide bridges

2.3. Ionic interactions

2.4. Van der Waals forces

Structural motifs and domains

3.1. β-barrel

3.2. Zinc finger

3.3. Helix–loop–helix

Chapter 3: Protein stability, folding and dynamics

Protein stability

Protein folding

Protein dynamics

Methods for studying dynamics

Chapter 4: Folding thermodynamics and kinetics

Folding code and thermodynamic principles

Folding kinetics

Folding models

3.1. Diffusion–collision

3.2. Nucleation–condensation

3.3. Zipping and assembly, ZA

3.4. Jigsaw puzzle model

3.5. Stoichiometric hypothesis, as named in the supplied source.

Methods for studying stability

4.1. Differential scanning calorimetry, DSC

4.2. Circular dichroism, CD

4.3. NMR, fluorescence and molecular dynamics

Chapter 5: Protein denaturation

Denaturing agents

Reversibility of folding

Functional consequences of denaturation

Chapter 6: Protein folding in vivo

Cellular folding mechanisms

Molecular chaperones

Disulfide bridge formation

Proline isomerisation

Conformational diseases, e.g. Alzheimer’s and Parkinson’s

Chapter 7: Engineering protein–ligand interactions

Principles

Physicochemical mechanisms

- Binding kinetics and thermodynamics

Molecular docking in silico

3.1. Docking definition

3.2. Docking types

3.3. Computational docking and modelling

3.4. Applications using PDB, ChemSketch, Chem 3D Ultra and other resources; PubMed, named in the source, is a literature database, not a ligand-structure database.

Chapter 8: Enzyme engineering

History

Enzyme design technology

Enzyme classification

Industrial applications

Enzyme production

5.1. Sources

5.2. Screening

5.3. Fermentation

5.4. Purification

Immobilised enzymes: principles and uses

Chapter 09: Chemical modification of proteins

Modification types

1.1. PEGylation

1.2. Glycosylation

1.3. Phosphorylation

Modification objectives

2.1. Stability

2.2. Half-life

2.3. Activity

2.4. Targeting

Experimental modification techniques

Course content

Workshop 1: Molecular identification of bacterial isolates

Extraction of bacterial genomic DNA

Quantitative and qualitative assessment of extracted DNA by electrophoresis and spectrophotometry

Amplification of the 16S rRNA gene and verification of amplification

Amplicon sequencing and in silico analysis: species-level identification of bacterial strains and phylogenetic tree construction

Workshop 2: Bacterial transformation

Students perform bacterial transformation of E. coli DH5α using a standard cloning vector to acquire genetic transfer and transformant selection skills.

Workshop 3: Random mutagenesis

Students induce random mutagenesis using different UV exposure durations, then screen for the optimal mutant producing a specific enzyme.

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

Chapter 1: Introduction to epigenetics

Conceptual and historical foundations

Definition and key concepts

History and development of the field

Chromatin architecture and nuclear organisation

Chromatin structure and levels of organisation

Methods for studying chromatin structure

Chapter 2: Histone modifications and recognition mechanisms

Histone modifications

Histone structure, diversity and nomenclature

Post-translational histone modifications

Enzymes responsible for histone modifications

Mechanisms recognising histone modifications

Protein recognition domains

The epigenetic histone code

Protein complexes associated with histone modifications

Chapter 3: DNA methylation and the role of noncoding RNAs

DNA methylation and related modifications

Biochemistry and distribution of DNA methylation

5-methylcytosine (5mC) and its derivatives

Genomic distribution: CpG islands and intergenic regions

Symmetric and asymmetric methylation

Non-CpG methylation in stem cells and neurons

Enzymatic machinery of DNA methylation

Maintenance DNA methyltransferase DNMT1

De-novo DNA methyltransferases DNMT3A and DNMT3B

DNMT3L and other cofactors

Targeting and regulation of DNMT activity

DNA demethylation: active and passive mechanisms

Proteins recognising DNA methylation

Noncoding RNAs and epigenetics

Types of noncoding RNA involved in epigenetic regulation

Long noncoding RNAs (lncRNAs)

Small interfering RNAs (siRNAs)

MicroRNAs (miRNAs)

Circular RNAs and other emerging classes

Epigenetic mechanisms of action of noncoding RNAs

Recruitment of chromatin-modifying machinery

Molecular scaffolding and formation of nuclear compartments

Targeting specific sequences through complementarity

Interactions with transcription factors

Examples of epigenetic regulation by noncoding RNAs

XIST and X-chromosome inactivation

HOTAIR and regulation of HOX genes

siRNAs and heterochromatin formation

Regulation by circular RNAs

Chapter 4: Epigenetics of development and differentiation

Epigenetic reprogramming

Cell differentiation and plasticity

Chapter 5: Environmental and transgenerational epigenetics

Environmental influences on the epigenome

Environmental factors modulating the epigenome

Molecular mechanisms of epigenetic responses to the environment

Principles and evidence of epigenetic inheritance

Potential mechanisms of transgenerational epigenetic transmission

Chapter 6: Epigenetics of disease

Cancer

Metabolic diseases

Cardiovascular diseases

Neurodegenerative diseases

Chapter 7: Methods for studying the epigenome

Methods for analysing histone modifications

Methods for analysing DNA methylation

Single-cell approaches

Chapter 8: Epigenetic therapies and new technologies

Course content

Chapter 1: General concepts, foundations and definitions

Essential definitions in cytogenetics

Structural and functional organisation of chromatin

Chromatin composition

Chromatin structure

Stages of chromatin condensation

Chapter 2: Specialised chromosome structures

Telomeres

Telomere structure

Replication of telomeric ends and the role of telomerase

Biological functions of telomeres

Centromeres

Structure of centromeric regions

The centromere paradox

Chapter 3: Chromosomal abnormalities

International nomenclature in human cytogenetics

General rules

Specific symbols and designations

Numerical chromosome abnormalities

Meiotic nondisjunction

Fertilisation-related abnormalities

Chromosomal mosaicism

Structural chromosome abnormalities

Reciprocal translocations

Robertsonian translocations

Deletions

Microdeletions

Ring chromosomes

Inversions

Isochromosomes

Insertions

Duplications

Dicentric chromosomes

Complex rearrangements

Marker chromosomes

Double-minute fragments

Chapter 4: Cytogenetic methods

Differences in cytogenetic protocols between organisms

Mammals

Plants

Yeasts

Other organisms

Factors affecting technical differences

Interpreting karyotypes

Molecular cytogenetic methods

Metaphase FISH

High-resolution FISH

Chromoprobe T FISH

M-FISH and spectral karyotyping (SKY)

Multicolour banding FISH

Metaphase comparative genomic hybridisation (CGH)

Array CGH: DNA microarrays

Primed in-situ labelling (PRINS)

Multiplex ligation-dependent probe amplification (MLPA)

Chapter 5: Chromosomal abnormalities in human genetic diseases and cancers

Karyotype alterations through chromosome gain or loss

Alterations of internal chromosome architecture

Chapter 6: Contributions of cytogenetics to molecular biology in animals, plants and yeasts

Animal cytogenetics

Diagnosis of genetic diseases

Evolutionary and phylogenetic studies

Plant cytogenetics

Varietal improvement

Plant evolution studies: origins of polyploid species

Cytogenetic monitoring of interspecific hybrids

Yeast cytogenetics

Differential chromosome compaction across cell-cycle phases in yeast

Modelling human diseases associated with chromosomal instability

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 DNA polymerases from different microorganisms.

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 molecular 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: Models in eukaryotic genetics

The nematode Caenorhabditis elegans

A model organism in molecular genetics: how its study helps explain the development of a multicellular organism.

Yeasts

S. cerevisiae and S. pombe as models for fundamental cell biology, from classical screens for conditional lethal mutations to recent genome-wide genetic approaches.

The fruit fly Drosophila melanogaster

Overview of Drosophila as a model for signalling pathways, development, neurobiology and immunology.

Overview of the Drosophila genome, chromosomes, including balancers, and genes.

Classical genetic screens

New technologies for spatial and temporal control of gene expression: GAL4/UAS and FLP/FRT.

Using these technologies for mosaic genetic screens and overexpression.

The mouse Mus musculus

A model of interest because of its functional proximity to humans; different mutagenesis and analytical approaches.

Value for studying complex functions, such as placental development, cellular homeostasis and metabolic homeostasis.

Development of new tools.

Plants

Arabidopsis thaliana as a molecular-biology model because of its genome size, ease of laboratory cultivation, rapid development and prolific reproduction.

Introduction to other plant models, including rice for monocotyledons and Physcomitrella patens for bryophytes.

Main molecular-genetic tools used to study model plants.

Chapter 2: Molecular bases of human genetic diseases

Positional cloning

Chromosomal abnormalities

Position-independent strategies for identifying disease genes

Testing a candidate gene identified through positional cloning

Identifying causal variants from association studies

Eight examples of identifying genes responsible for diseases or traits:

Case 1: Duchenne muscular dystrophy

Case 2: Cystic fibrosis

Case 3: Branchio-oto-renal syndrome

Case 4: Multiple sulfatase deficiency

Case 5: Intestinal lactase persistence

Case 6: CHARGE syndrome

Case 7: Breast cancer

Case 8: Crohn's disease

Progress in identifying disease genes

Alzheimer's disease

Age-related macular degeneration

Eczema: atopic dermatitis

AI for disease prediction: TPOT and AutoML

Chapter 3: Cancer genetics

Cancer development

Oncogenes

Tumour suppressor genes

Abnormal cell-cycle regulation in cancer

Genome instability

Cancer and whole-genome studies

Understanding multistep tumour development

Data integration: cancer in cell-biological terms

AI for early diagnosis and cancer-biomarker detection; the programme discusses PathAI and IBM Watson for Oncology.

Course content:

Lecture programme

Chapter 1: Foundations of bioinformatics

Computing in biology and medicine;

Introduction to Unix and Linux systems and basic commands;

Database concepts;

Protein and nucleic acid databases;

Structural databases;

Biological XML document type definitions (DTDs);

Fundamentals of pattern-matching algorithms;

Databases and search tools: biological context for sequence analysis;

Identifying protein sequences from DNA sequences;

Searching databases for similar sequences;

NCBI;

Publicly accessible tools;

Resources at EMBL-EBI;

Web resources;

Database exploration tools

Chapter 2: DNA sequence analysis

DNA sequence analysis: gene sequence databases

Submission and searching of DNA sequences in databases

Sequence alignment;

Pairwise alignment techniques;

Motif discovery and gene prediction;

Local structural variations in DNA, their relevance to molecular processes and their identification;

Assembly of genome sequencing data.

Multiple sequence analysis

Multiple sequence analysis;

Multiple sequence alignment;

Flexible sequence similarity searching with the FASTA3 package;

Using CLUSTALW and CLUSTALX for multiple sequence alignment; submission of DNA and protein sequences to databases:

Submission methods;

SEQUIN;

Genome centres;

Submission of aligned sequence sets;

Updating submitted sequences;

Phylogenetic analysis methods.

Practical programme:

Sequence searches in databases using BLAST, GenBank and RefSeq

Primer design using Primer3

PCR or cloning simulation using SnapGene

Pairwise and multiple sequence alignment using BLAST

Phylogenetic tree construction using MEGA

Genome assembly and annotation using Geneious

Module content

Chapter 1: Review of the molecular organisation of biomembranes

Biomembrane structure

Asymmetry of membrane lipid composition and distribution

Distribution of membrane proteins

Membrane fluidity

Targeting mechanisms

Intracellular vesicular trafficking of proteins

Post-translational protein modifications

Lipidation

Glycosylation

Chapter 2: 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

Receptor tyrosine kinases (RTKs)

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

SH domains (Src homology domains)

PTB domains (phosphotyrosine binding)

3.1.2. SH2-domain adaptor proteins

Grb2 protein

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

Cyclic AMP and adenylyl cyclase

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

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

Cyclic GMP and guanylyl cyclase

Protein kinases

Phosphorylation reactions and kinase domains

Major protein kinases

Protein kinase A (PKA)

Protein kinase C (PKC)

Protein kinase B (Akt)

Mitogen-activated protein kinases (MAPKs)

Chapter 3: 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 4: 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 s 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 5: 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 6: 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

Generative AI and prospective modelling of signalling pathways

Course content

Chapter 1: General introduction

Enzyme engineering

Biological engineering

Chapter 2: Reactors and reaction processes

Definition of a chemical reactor

Reactor classification

Nature of the reaction medium

Reactor operating mode

Activation and chemical transformation modes

Definition of reaction quantities

Conversion

Extent of reaction

Residence time

Microbiological processes

Biological process yields in reactors: microbial growth kinetics models

Batch bacterial growth kinetics model

Continuous bacterial growth kinetics model

Biological process yields in batch and continuous reactors

Substrate-to-biomass conversion yield

Metabolite production yield

Chapter 3: Reactor modelling

Modelling a reactor with non-renewed medium

Modelling a continuous, perfectly mixed biological system with and without recycle

Continuous operation without biomass recycle

Continuous operation with biomass recycle

Two-stage, perfectly mixed continuous systems

Chapter 4: Processes in enzyme reactors

Enzyme reactors and enzyme immobilisation concept

Fixed-bed reactors

Fluidised-bed reactors

Enzyme immobilisation

Sizing enzymatic bioreactors

Bioreaction apparatus

Reactor jacket

Agitation system

Process performance in enzymatic bioreactors

Kinetic performance

Detecting enzyme activity

Chapter 5: Sterilisation

Sterilisation process

Autoclave sterilisation

Continuous monitoring of the sterilisation cycle

Sterilisation methods

Closed batch system

Ethylene oxide sterilisation

Continuous system

Dry-heat sterilisation

Chapter 6: Scale-up from laboratory through pilot to industrial scale

Scale-up stages

Challenges of bioprocess scale-up

Chemical critical points

Physical critical points

Resolving and limiting critical-point impacts during scale-up

Laboratory to industry: polymer synthesis case study; 6.2.1 Biological critical points, as ordered in the source

Chapter 7: Bioseparation engineering

Classification of bioseparation processes

Mechanical separation processes

Wettability

Mass density

Particle size

Electrical mobility

Diffusion-based separation processes

Chapter 8: Idealised recovery process

Stages of an idealised recovery process

Primary separation or harvesting

Filtration

Acid/surfactant lysis and organic-phase absorption as worded in the source

Flocculation and precipitation

Isolation or capture of the target molecule

Ion-exchange chromatography

Affinity chromatography

Purification

Polishing

Size-exclusion chromatography

Hydrophobic-interaction chromatography

Bioconjugation and formulation

Chapter 9: Separation devices in industrial cell culture

Continuous perfusion reactor with cell retention

Continuous perfusion reactor retaining cells with hollow fibres or membranes

Continuous perfusion device retaining cells with resonant ultrasound waves

Chapter 10: Critical analysis of cell-retention perfusion reactors in industry

Advantages of each design in industrial settings

Continuous cell-retention perfusion reactor with hollow fibres or membranes

Continuous cell-retention perfusion reactor using resonant ultrasound waves

Limitations of each industrial design

Continuous cell-retention perfusion reactor with hollow fibres or membranes

Continuous cell-retention perfusion reactor using resonant ultrasound waves

Course content

Workshop 1: Genomic DNA extraction

Workshop 2: Quantitative and qualitative assessment of extracted DNA

Workshop 3: PCR-RFLP

Workshop 4: Multiplex PCR

Workshop 5: Allele-specific PCR

Workshop 6: PCR-SSCP

Workshop 7: qPCR

Course content

Experimental techniques

The workshop applies the following key techniques:

Measure activity using a method appropriate to the enzyme studied and extracted.

Measure total protein by the Bradford method.

Produce the enzyme by submerged fermentation, SMF.

Fractional precipitation with ammonium sulfate.

Desalt by dialysis, followed by size-exclusion/gel-filtration and affinity chromatography.

Evaluate purification using SDS–polyacrylamide gel electrophoresis, SDS-PAGE; the source incorrectly calls this an agarose gel.

Workshop organisation and schedule

Workshop 1: Preparation of solutions and culture media

Opening and explanation

Laboratory safety reminders

Workshop 2: Enzyme production by submerged fermentation, e.g. bacterial or fungal α-amylase or another enzyme

Qualitative demonstration of production, e.g. starch hydrolysis.

Enzyme extraction.

Quantitative enzyme and protein assays.

Workshop 3: Enzyme purification

Fractional precipitation with ammonium sulfate.

Remove ammonium sulfate by dialysis.

Size-exclusion chromatography.

Affinity chromatography.

Workshop 4: Assessment of purification

Purification table.

SDS-PAGE.

Workshop 5: Enzyme characterisation and effects of physicochemical factors on activity and stability

Workshop 6: Determination of kinetic parameters

Module content

Chapter 1: Fundamentals of nanotechnologies applied to biology

Definitions, scales and properties of nanomaterials.

History and development of nanobiotechnology in biology.

Fabrication approaches: top-down versus bottom-up.

Biotechnology examples (polymeric nanoparticles, liposomes, quantum dots, etc.).

Nanoparticle functionalisation for biological applications.

Surface modifications

Cell targeting

Fluorescence

Molecular conjugation

Types of nanodevices used in biotechnology

Metallic, polymeric and lipid nanoparticles

Nanosensors

Nanopores and functionalised nanoprobes

The three main fields of nanotechnology

Nanomaterials: properties, synthesis, characterisation and biomedical applications

Nanoelectronics: sensors, nanoscale circuits and integration into omics platforms

Nanobiotechnologies: convergence of nanotechnology, molecular biology and spatial biology

Chapter 2: Introduction to spatial biology and omics

Introduction to spatial omics technologies

Spatial transcriptomics: Visium, CosMx, Xenium and MERSCOPE

Spatial proteomics: MACSima and MIBIµ

Single-cell analysis: scRNA-seq and ATAC-seq

Associated techniques: immunohistochemistry, RNA-seq and multiplex imaging

Major technological platforms

GeoMx Digital Spatial Profiler

MERSCOPE and hybrid methods

Visium HD, Xenium and CosMx: performance comparison

Application areas

Cancer and tumour heterogeneity

Neuroscience and mapping of brain tissues

Immunology, inflammation and infectious diseases

Chapter 3: Nanodevices integrated into spatial omics technologies

Nanoscale sensors for multiplex imaging and signal amplification

Functionalised nanobeads (Xenium and CosMx, as exemplified in the programme)

Amplification using gold or silver nanoparticles

Multiplexed nanomaterial-based probes

Nanostructures for molecular capture, delivery and labelling

DNA, RNA and proteins

Case studies: nanoscale components in Visium HD or Xenium and their contribution to detection performance

Chapter 4: Biomedical applications and outlook

Contribution of nanotechnologies to spatial single-cell diagnostics

Technological and bioethical challenges of nano-omics integration

Towards precision medicine enhanced by nano/omics/spatial convergence

Course content

1. Patenting an invention

1.1. Introduction to intellectual property rights

1.2. Forms of intellectual property rights

A. Industrial property

- Patents

- Designs

- Registered trademarks

- Geographical indications

B. Non-industrial property

- Copyright ©

2. History and evolution of patent law

2.1. Development of patent legislation

2.2. History of the Algerian patent system

2.3. International conventions and treaties

2.4. Patent laws in other countries

3. Patent classification

3.1. Classification in Algeria

3.2. WIPO patent classification

3.3. Patent categories

3.4. Special patents

3.5. Biological product patents

4. General legislative provisions for patents in Algeria

4.1. Patentability: what can be patented?

4.2. Exclusions from patentability

4.3. Entitlement to a patent

4.4. Employee inventions

4.5. Unity of invention

4.6. Certificate of addition

5. Patent application and grant procedures

5.1. Filing

5.2. Examination

5.3. Grant

5.4. Maintaining patent validity

6. National patent system

6.1. Algerian National Institute of Industrial Property, INAPI

6.2. Patent application formalities

7. Filing a patent application abroad

7.1. Protecting an invention in several countries

7.2. Patent Cooperation Treaty, PCT

7.3. Advantages of the PCT

7.4. Filing an international application under the PCT

8. Patent holders: rights and duties

8.1. Patent ownership

8.2. Rights of owners and co-owners

8.3. Obligations of owners and co-owners

8.4. Transfer of patent rights

8.5. Limitations on patent rights

8.6. Restoration of patent rights

8.7. Patent infringement and offences

8.8. Infringement proceedings and remedies

9. Patenting life forms

14.1. Introduction

14.2. Patent grant criteria

14.2.1. Patentability prerequisites

14.2.2. Essential patentability requirements

14.3. Cell and cell-line patents

14.4. Gene and DNA sequence patents

14.4.1. Sequences for diagnostic tests

14.4.2. Sequences as research tools

14.4.3. Sequences for gene therapy

14.4.4. Sequences for therapeutic protein production

14.5. Animal patents

14.6. Protection of new plant varieties

14.6.1. Patents

14.6.2. Sui generis protection: International Union for the Protection of New Varieties of Plants, UPOV

14.6.3. Geographical indications

10. Biopharmaceutical patents

10.1. Overview

10.2. Pharmaceutical and biopharmaceutical products

10.2.1. Biologics versus conventional drugs

10.2.2. Biosimilars and “interchangeable” biologics

10.3. Rationale for biopharmaceutical IP protection

10.4. Patent protection for biologics

10.4.1. Incremental innovation

10.4.2. Evergreening

10.5. Patent protection for diagnostics

10.6. Effects of patent protection on genetic testing

10.7. International trade agreements on medicines

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: Genetic engineering

Grammar: Modal verbs.

Vocabulary: genetic 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 GMO applications using modal verbs.

Unit 5: The future of Genetic engineering.

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 genome editing.

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

Course content

Foundations of genomics and proteomics

Overview of prokaryotic and eukaryotic genome organisation

Extrachromosomal DNA: bacterial plasmids, mitochondria and chloroplasts.

Genome mapping

Genetic and physical maps

Markers for genetic mapping

Methods and techniques used for genetic mapping

Physical mapping

Linkage analysis

Cytogenetic techniques

Fluorescence in situ hybridization (FISH) in genetic mapping

Somatic cell hybridization

Radiation hybrid maps

In situ hybridization

Comparative genetic mapping

Genome sequencing projects

The Human Genome Project

Microbial, plant and animal genome sequencing projects

Accessing and retrieving information about genome projects from the web

Comparative genomics

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

Using genomes to understand eukaryotic evolution

Monitoring emerging diseases and designing new medicines

Determining gene locations within a genome sequence

Transcriptomics

Introduction

Data acquisition

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

Microarrays

qPCR, RT-PCR and qRT-PCR

Data description

Transformation, normalization and filtering

Transcriptome data analysis

Differentially expressed genes

Co-expressed genes

Interpretation

Characterization of a gene set

Proteomics

Aims

Strategies and challenges in proteomics

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

Proteomic databases

Functional genomics and proteomics

Transcriptome analysis for gene identification and functional annotation

Contig assembly

Chromosome walking and chromosome characterization

Identification of functional genes in the genome

Gene function

Forward and reverse genetics

Protein–protein and protein–DNA interactions

Protein microarrays and functional proteomics

Biomedical and clinical applications of proteomics

Introduction to metabolomics, lipidomics, metagenomics and systems biology

Artificial intelligence applied to omics data

Introduction to artificial intelligence applied to omics data

Basic concepts: machine learning, deep learning and neural networks

General applications in biological sciences

AI in genomics

Prediction of genes and functional elements in the genome

Automatic sequence annotation and classification

Large-scale comparative genome analysis

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.

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

Chapter I: History of genetic engineering

Chapter II: Enzymatic tools of genetic engineering

2.1. Restriction enzymes

Restriction phenomenon

Recognition sites

Isoschizomers

Restriction–modification system, RM

Origins of restriction enzymes

Restriction enzyme nomenclature

Types of restriction enzyme cleavage

Classes of restriction enzymes

Methylation of restriction sites and restriction enzyme inactivation

Uses of restriction enzymes

2.2. Other enzymes commonly used in genetic engineering

Polymerases

Ligases

Alkaline phosphatases

Nucleases

Other specific enzymes

Chapter III: Molecular hybridisation

3.1. Review of hybridisation principles

DNA melting temperature

Factors affecting melting temperature

3.2. Molecular hybridisation

Liquid-phase hybridisation

Solid-support hybridisation

3.3. In situ hybridisation

3.4. Probes

Principles of nucleic acid hybridisation

Probe concept

Labelling strategies

Labelling long nucleic acid probes with labelled nucleotides

DNA labelling by nick translation

Random-primed DNA labelling

Labelling during PCR strand synthesis

RNA labelling

Nucleic acid labelling with radioactive isotopes

Non-isotopic nucleic acid labelling with fluorophores

Chapter IV: Vectors

4.1. General principles of vectors

Vector concept and properties

General principles of vector use

4.2. Plasmids

Using a plasmid

Plasmid preparation

Different plasmid types

First-generation plasmids

Second-generation plasmids

Third-generation plasmids

Origin of replication

4.3. Phages

Phage use

Phage preparation

Phages used in molecular biology

First-generation phages: λ phage

Second-generation phages

4.4. Other vector types

Cosmids

Artificial chromosomes

Yeast artificial chromosome, YAC

Bacterial artificial chromosome, BAC

Shuttle vectors

Eukaryotic viral vectors

Chapter V: Cloning and recombinant protein expression

5.1. Cloning principles

PCR-based cloning

Designing PCR primers for cloning

Choosing restriction enzymes

Cloning stages

5.2. DNA libraries

Genomic DNA libraries

cDNA libraries

5.3. Expression systems

Choosing an expression system

Post-translational modifications

Prokaryotic expression system

5.4. Genetic expression cassette for recombinant proteins

5.5. Characteristics of E. coli

5.6. Overview of heterologous protein expression in E. coli

5.7. Recombinant protein expression

Chapter VI: Genetically modified organisms, GMOs

6.1. Plant transgenesis

Plant transgenesis and conventional breeding methods

Plant transgenesis techniques

Production of genetically modified plants

Conditions for successful plant transgenesis

Transformation techniques

Direct transfer

Indirect transfer

6.2. Animal transgenesis

Definition

Gene transfer methods in animals

Gene transfer into one-cell embryos

Gene transfer via embryonic cells

Gene transfer into gametes

Using sperm-cell precursors

Gene transfer into somatic cells

Gene transfer into mitochondria

Other recent gene transfer techniques

6.3. Constructing a transgene

6.4. Other techniques for creating GMOs

6.5. Main GMO applications

6.6. GMO traceability and labelling

Chapter VII: New genetic engineering techniques and applications

7.1. Genome editing

7.2. Programmable nucleases

7.3. RNA interference

7.4. Zinc-finger nucleases

7.5. TALENs

7.6. CRISPR/Cas9

Chapter VIII: Biosafety and bioethics in genetic engineering

Introduction to biosafety

Fundamental concepts

Biological risk assessment

Cartagena Protocol

GMOs and biosafety issues

GMO regulatory frameworks

Biosafety of recombinant DNA-derived products

Risk analysis and management

Safety assessment: foods, animals and clinical trials

Precautionary principle

Laboratory and industrial biosafety

Bioethics concepts

Course content

General introduction to personalised medicine

Clinical research and pharmacogenetics

Genetic testing and phenotyping

Advances in pharmacogenomics

The role of biomarkers across different fields and in oncology

New approaches

Genetics

Proteomics

Metabolomics

Microbiota

Epigenetics

Next-generation sequencing (NGS): exome sequencing.

Germline pharmacogenomics

Genetics-based personalised medicine

Personalised medicine and its current clinical applications

Fields covered: cardiovascular medicine, pain pharmacology, psychiatry, pharmacogenetics in rheumatology, adverse effects, drug interactions, drug-induced liver injury (DILI) and cancer genetics.

Molecular docking

Molecular docking and pharmacogenetics

Principles of molecular docking

Applications of docking in pharmacogenetics

Artificial intelligence for docking in pharmacogenetics

Contributions of artificial intelligence to pharmacogenetics

Random forests, support vector machines (SVMs) and neural networks for modelling multi-omics data.

Deep learning for exome sequence analysis using NGS and automated detection of clinically relevant variants.

AI-based prediction of treatment response. Study of CancerCellNet for cancer-model classification and assessment of transcriptional fidelity to tumours.

Natural language processing (NLP) to extract relevant information from medical publications.

Industrial perspectives and development of companion diagnostic tests for targeted therapies.

From protocol drafting to methodological support and implementation.

Research valorisation, patent jurisdiction and practical experience.

Course content:

Chapter 1: Review of immunology fundamentals

Components of the immune system

Innate and adaptive immunity

The immune system in action

Chapter 2: The major histocompatibility complex, MHC, and human leukocyte antigen system, HLA

Role and function

Structure of the HLA system

Genetic aspects

Immunological aspects

Chapter 7: Immunogenetics and transplantation

Classical HLA and organ transplantation

Classical HLA and bone marrow transplantation

Non-classical HLA class I and organ transplantation

Non-classical HLA class I and bone marrow transplantation

Graft-versus-host reaction

HLA typing

Chapter 3: Immunoglobulins

Role and function

Structure of the immunoglobulin system

Genetic aspects

Immunological aspects

Chapter 5: Comparative immunogenetics: evolution of polymorphism in genes involved in immune responses

Classical HLA polymorphism

Non-classical HLA polymorphism; the programme cites MICA and MICB, which are MHC class I-related molecules.

Toll-like receptor, TLR, polymorphism

Chapter 6: Immunogenetics and immunopathology

Autoimmune diabetes

Genetics of type I diabetes

Relationships between polymorphisms and immune-mediated diseases

Chapter 8: Immunoinformatics

Introduction to immunoinformatics

IMGT: the international ImMunoGeneTics information system

Chapter 9: Biotherapies and targeted therapy

Definition

Role and function

Mechanism of action

Examples of biotherapies and targeted therapies

Chapter 10: Immunotherapies from bench to clinic

Immunology in biotherapy

Clinical trial methodology and statistics

Principles of clinical trials

Production of haematopoietic cells

Quality and regulatory requirements in biotherapies

Chapter 11: Monoclonal and polyclonal antibodies

Using the immunomodulatory properties of invariant natural killer T cells, iNKT cells, in immunotherapy

Physicochemistry of non-viral gene therapy vectors

Anti-HIV vaccine strategies

Antigen design and antitumour vaccination

Mechanisms of cutaneous desensitisation

Virosomes and anti-HIV vaccine applications

Chapter 12: Gene therapy: genetic approaches to treating disease

Treatment of genetic diseases versus genetic treatment of diseases

Principles and applications of cell therapy

Stem-cell-based therapies

Embryonic stem cells

Tissue stem cells

Practical difficulties of stem-cell therapy

Allogeneic or autologous cell therapy

Nuclear reprogramming

Induced pluripotency in somatic cells

Transdifferentiation

Genetic approaches to disease treatment using drugs, recombinant proteins and vaccines

Identifying new drug targets

Therapeutic protein production by expression cloning in microbes, mammalian cell lines or transgenic animals

Engineering new antibodies with therapeutic potential

Producing vaccines and improving their function through genetic engineering

Production of cancer vaccines

Gene therapy principles and mammalian gene transfection systems

Genes can be transferred into patient cells in culture or within tissues

Integration of therapeutic genes into chromosomes; the source sentence is incomplete.

Using viral vectors for gene transfer

Retroviral vectors

Using adenoviruses and adeno-associated viruses, AAVs, as vectors

Other viral vectors

Non-viral vector systems

Nucleic acid transfer by direct injection or particle bombardment

Lipid-mediated gene transfer

Compacted DNA nanoparticles

RNA- and oligonucleotide-based therapeutics and therapeutic gene repair

Selective inactivation of a mutant allele

Therapeutic ribozymes

Therapeutic small interfering RNAs, siRNAs

Inducing exon skipping with antisense oligonucleotides

Gene targeting with a zinc-finger nuclease

Gene therapy in practice

Gene therapy for recessive inherited diseases of blood cells

Gene therapies for other monogenic diseases

Cancer gene therapy

HIV gene therapy

Course content

Session 1: 05 hours

Prepare solutions and culture media.

Design cloning primers.

Session 2: 06 hours

Extract genomic DNA using a kit.

PCR cloning of the target gene.

Simulate target-gene cloning in silico with SnapGene.

Qualitative and quantitative checks: agarose gel electrophoresis.

Session 3: 06 hours

Purify the PCR product and quantify DNA.

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

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

Electrophorese digestion products, then purify them from agarose gel.

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

Screen transformed clones in the presence of antibiotic.

Lecture on recombinant DNA technology.

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

Session 7: 06 hours

Recombinant enzyme expression tests, part 01: prepare 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 with a HisTrap affinity chromatography column.

SDS-PAGE.

Session 10: 08 hours

Confirm recombinant protein identity by Western blotting.

Test the expressed protein’s biological activity.

Analyse results.

Course content

Part 1: Introducing Arduino

Definition

Purpose and usefulness

Applications

Reasons for choosing Arduino

Arduino tools

Hardware: UNO board and ATMega microcontroller.

Software: Arduino IDE, compilation and uploading.

Programming

What is a program?

Creating a computer program.

Compiler role.

Programming for electronics

Introduction to microcontrollers.

Internal microcontroller components

Central processing unit, CPU.

Memory: Flash, RAM, EEPROM, cache and registers; components depend on the microcontroller.

Arduino IDE software

Hardware: Arduino UNO board

Introducing the board.

Main features: pins, voltage and memory.

Digital and analogue signals

Sensors and detectors

Teaching distinction between continuous-measurement sensors and binary-state detectors.

Examples: temperature sensor and presence detector.

Number bases 2, 10 and 16

Base 10: decimal.

Base 2: binary.

Base 16: hexadecimal.

Conversion summary table.

Conversions

Decimal ↔ binary.

Binary ↔ hexadecimal.

Arduino language

Language syntax

Minimal code: setup() and loop().

Statements: semicolons, braces and comments.

Data, variables and constants

Types: int, float and String.

Declaration examples.

Program structure commands

Digital/analogue inputs and outputs.

Time management: delay() and millis().

Arithmetic, logical and assignment operators.

Control structures

Conditions: if/else.

Loops: while and for.

LCD screen

Display types: alphanumeric and graphical.

Wiring: parallel/semi-parallel communication as worded in the source.

Programming with LiquidCrystal.

Part 2: pH meter

Definition of a pH meter

Electrodes

Glass electrode tip types: spherical, conical, flat and spear/cutting.

Reference electrodes: calomel, mercurous sulfate and silver chloride.

Operating principle

Potential difference and the Nernst equation.

Acidic/neutral/basic classification.

Electrode measurement chain

Calculating parameters a and b.

pH meter calibration

Temperature effects

Practical work

Simulation with Arduino and an LCD screen.

Data acquisition and calibration program.

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

I – Metagenomics

1 – Introduction to metagenomics

2 – Metagenomic strategies

– Whole-community metagenomics

– Targeted metagenomics

– 16S ribosomal RNA

3 – Taxonomic assignment

– Closed-reference strategy

– De novo strategy

– Operational taxonomic unit table

4 – Data analysis

– Alpha diversity

– Beta diversity

II – The microbiota

1 – Introduction to the microbiota

– Structure and function

– Diversity of the healthy human microbiota

2 – Microbiota dysbiosis

– Highly abundant functions contributed by low-abundance microbes

– Phylogenetic and functional variation between enterotypes

– Host-associated functional biomarkers

– Correlations with the host phenotype

– Relationship between metabolism and the microbiota

III – The microbiota metagenome

1 – Overall phylogenetic and functional variation in intestinal metagenomes

2 – Bacterial genomics and metagenomics: clinical applications and medical importance

3 – Diagnostic tools

– Development of molecular diagnostic tools

– Development of serological tools

4 – Antibiotic resistance

5 – Epidemiology and dissemination of multidrug-resistant bacteria

Tutorials

Article analysis

Statistical analysis of metagenomic data using R

Course content

Concepts

History of synthetic biology

Foundations of synthetic biology

Engineering living systems

Tools and approaches in synthetic biology

Chemistry, biochemistry and recoding of living systems

Metabolic engineering

DNA sequencing and fabrication: basic building blocks

Genetic rewriting

Introduction to xeno nucleic acids

Mathematical modelling

Measurements: microscopy and flow cytometry

Design of customised metabolic pathways

Design of regulatory systems

Applications

Future challenges in synthetic biology

Safety, social and ethical aspects

Course content

Theoretical component:

Plant biotechnology

1.1. A brief history of plant biotechnology

1.2. Traditional plant improvement methods

Plant transgenesis

Indirect DNA transfer to plant cells mediated by Agrobacterium

Discovery of the Ti plasmid

From pathogen to transformation vector: stages of plant-cell infection by A. tumefaciens

Indirect DNA transfer: practical applications of Agrobacterium-mediated plant transformation

Direct DNA transfer to plant cells

Particle bombardment

Electroporation

Whiskers

Direct DNA uptake

A toolkit for plant genetic engineering

Tools for gene overexpression and downregulation

Using transgenic plants in research and development strategies

Tools for controlling target-gene expression in space and time: constitutive, inducible and tissue-specific promoters; terminators; other construct elements related to transgene expression and intracellular targeting; and selection markers.

Strategies for rational modification of gene expression: sense and antisense strategies, ribozymes, co-suppression and RNA interference.

Strategies for plant gene discovery: activation tagging, random mutagenesis, targeted mutagenesis and genome editing, and promoter discovery.

Biosafety and bioethics in plant biotechnology

Biological risks

Uncontrolled transfer of genetic material between modified and unmodified crops

Effects on biodiversity and emergence of resistance

Biosafety measures

Biological containment

Buffer zones

Post-cultivation monitoring

Application of the Cartagena Protocol and the precautionary principle

Ethical considerations

Preserving biodiversity and protecting local agriculture

Respecting informed consent

Equitable access to innovations and transparency regarding genetically modified organisms

Practical work

Totipotency

Protoplast isolation and fusion

Preparing a karyotype

Haploid production and chromosome doubling

Course content

Chapter 1: Introduction to process design

Chapter 2: Principles of bioprocess engineering

Industrial bioprocesses: biocatalysis, unit operations and applications

Bioprocess design

Bioprocess modelling and simulation

Economic and environmental optimisation of bioprocesses

Case study: mass balance of a bioprocess

Chapter 3: Bioprocesses and recombinant protein production

Industrial enzymatic bioconversions

Design of a continuous bioprocess coupling recombinant protein production and purification

Modelling and simulation of a bioreactor for recombinant protein expression

Case study: an industrial process for recombinant vaccine production

Chapter 4: Microbial fermentation processes

Industrial microbial fermentations

Design of microbial fermentation processes

Modelling and simulation of an enzymatic bioreactor

Case study: an industrial process for producing a recombinant protein by fermentation

Chapter 5: Purification processes — downstream processing (DSP)

Overall approach to downstream processing

Main purification unit operations in bioprocesses

DSP process design and technology selection

Case studies: industrial lysine purification

Note: The case studies listed are indicative and may vary.

Course content

Step 01: Cell culture and irradiation

Isolation of peripheral blood mononuclear cells (PBMCs) by Ficoll® density-gradient centrifugation.

Exposure of PBMCs from healthy donors’ peripheral blood to ultraviolet radiation.

Culture of these cells at 37°C and 5% CO2.

Harvesting of cells at different times for gene and protein analyses.

Step 02: Investigating the effect of irradiation on p53 gene expression

Extraction of total RNA

DNase treatment

RNA quantification

Reverse transcription of mRNA into cDNA (RT-PCR)

Quantification of mRNA using real-time PCR (qPCR)

Analysis and interpretation of results

Step 03: Investigating the effect of irradiation on p53 and phosphorylated p53 protein expression

Lysis of cultured cells

Protein assay using Bradford reagent

Sample preparation

Polyacrylamide gel electrophoresis

Transfer of proteins to a membrane

Immunodetection using a specific primary antibody and a conjugated secondary antibody

Signal development and interpretation of results

Band quantification

Course content

Mini-project topics are proposed by teaching staff and/or students. Each applies at least one field taught in earlier semesters—genetic, biochemical, microbial or enzyme engineering, or bioinformatics—to a problem or original application in industry, pharmaceuticals, medicine or a related field.

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

Chapter 1: Principles and challenges of reverse engineering in the life sciences

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.

1.2. 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

3.1. The right to reverse engineer in relation to patents

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

International comparative analysis

Summary table:

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.

Chapter 2: Integrated approaches to reverse engineering, bioinformatics and biological systems modelling

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.

Bioinformatics and free software in the biological sciences

2.1. 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.

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.

Reverse engineering of genetic tools

Plasmid analysis and reverse engineering using Benchling and SnapGene Viewer.

Engineering promoters and reporter genes.

Workshop: reverse-designing an optimised genetic construct for bacterial expression.

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