Enzyme Engineering

Chapter

Title

Content

1

Introduction to Enzymology

1. Historical background 2. Definition and significance of enzymes 3. Overview of enzyme structure 4. Properties and characteristics of enzymes 5. Cellular localization of enzymes 6. Enzyme size and molecular weight 7. Enzyme nomenclature and classification

2

Structure–Function Relationship

1. Functional architecture of enzymes 2. Isoenzymes and their physiological roles 3. The active site: composition and topology 4. Substrate binding site vs. catalytic site 5. Role of amino acid residues at the active site 6. Factors influencing enzyme-substrate binding 7. Enzyme-substrate interaction models (lock-and-key, induced fit) 8. Types of non-covalent interactions

3

The Enzymatic Reaction

1. Definition and general principles 2. Mechanistic steps of enzyme-catalyzed reactions 3. Key elements in enzymatic reactions 4. Influencing factors 5. Reactions involving two substrates

4

Energetics of Enzyme-Catalyzed Reactions

1. Activation energy (Ea) 2. Transition state theory 3. Enthalpy change (ΔH) 4. Gibbs free energy (ΔG) 5. Spontaneity and reversibility of reactions

5

Enzyme Kinetics

1. Introduction to enzyme kinetics 2. Basic principles of chemical kinetics 3. Phases of enzyme-catalyzed reactions 4. Initial reaction velocity (V₀) 5. Michaelis-Menten kinetics 6. Enzyme kinetic parameters (Km, Vmax) 7. Lineweaver-Burk plot and kinetic linearization methods

6

Molecular Mechanisms of Enzymatic Catalysis

1. Proximity and orientation effects 2. Covalent catalysis 3. Acid-base catalysis 4. Metal ion catalysis

7

Enzyme Inhibition

1. Introduction to enzyme inhibition 2. Role of effectors in modulation 3. Types of enzyme inhibitors 4. Design and application of enzyme inhibitors in biotechnology and medicine

8

Enzyme Regulation

1. Overview of enzyme regulation 2. Regulatory enzymes and their functions 3. Mechanisms of regulation

Tutorial

Title

Focus

1

Enzyme Activity Quantification

Introduction to methods for measuring enzyme activity (e.g., spectrophotometric assays, unit definitions)

2

Enzyme Activity Quantification – Exercises

Practice calculations involving enzyme units, specific activity, and reaction rates

3

Enzyme Kinetics – Exercises

Analyze enzyme-catalyzed reaction rates using Michaelis-Menten and Lineweaver-Burk plots

4

Enzyme Inhibition – Exercises

Solve problems involving competitive, non-competitive, and uncompetitive inhibition; determine Km and Vmax changes

Session

Title

Objective

Key Activities

Key Techniques

1

Introduction to Enzymes & Assay Setup

Learn to prepare and standardize enzyme assays.

• Extract or produce a simple enzyme • Perform a Bradford assay for protein quantification • Set up a basic enzyme activity assay • Calculate enzyme activity

• Spectrophotometry • Pipetting • Calibration curves

2

Effects of pH and Temperature

Explore how environmental factors affect enzyme activity.

• Measure enzyme activity across pH range (2–10) • Test activity at different temperatures (10°C–70°C) • Discuss denaturation and transition-state theory

• Buffering • Temperature control

7

Enzyme Kinetics (Michaelis-Menten)

Determine Km and Vmax for an enzyme.

• Measure reaction rates at various substrate concentrations • Plot Michaelis-Menten and Lineweaver-Burk curves • Interpret kinetic parameters

• Data linearization • Curve fitting • Kinetic parameter calculation

8

Enzyme Inhibition

Characterize competitive vs. non-competitive inhibition.

• Test a model enzyme with inhibitors • Compare reaction rates with/without inhibitors • Use Lineweaver-Burk plots to classify inhibition type

• Inhibitor preparation • Kinetic modeling

Chapter

Title

Content

1

Introduction to Molecular Biology

Historical background and importance; Central dogma of molecular biology

2

Structure of Nucleic Acids

Chemical components of nucleic acids; Nucleosides and nucleotides; Nucleotide polymerization; DNA structure and organization; RNA structure, types, and functions; Manipulation of nucleic acids

3

Genome and Gene Organization

Key concepts; Genome organization; Gene organization

4

DNA Replication

Principles of DNA replication; Enzymes involved in replication; DNA replication in prokaryotes and eukaryotes

5

Genetic Variation and DNA Maintenance

DNA integrity; DNA damage; Cellular responses to DNA damage; DNA repair mechanisms; Genetic variation and mutations

6

DNA Transcription

Principles of transcription; Transcription unit; Transcription in prokaryotes and eukaryotes

7

Translation of mRNA

Genetic code; Components of the translation machinery; Translation in prokaryotes and eukaryotes; Post-translational modifications

8

Introduction to AI Applications in Molecular Biology

Fundamentals of artificial intelligence, machine learning, and deep learning; Biological databases; Bioinformatics tools; AI-assisted sequence analysis and structure prediction; Genome annotation; AI applications in gene regulation and protein analysis

Worksheet

Title

Key Activities / Topics

01

Structure of Nucleic Acids

• Chemical structure of DNA and RNA • Nucleotides, base pairing, phosphodiester bonds • DNA double helix and RNA types

02

Genome and Gene Organization

• Prokaryotic vs. eukaryotic genomes • Gene structure and types • Transposable elements and genome dynamics

03

DNA Replication

• Mechanisms in prokaryotes and eukaryotes • Enzymes involved in replication • Origin of replication and replication fork

04

Genetic Variation and DNA Maintenance

• Endogenous/exogenous DNA damage • DNA repair pathways • Types of mutations and their effects

05

DNA Transcription

• Template vs. coding strand • RNA polymerase activity • Transcription process in prokaryotes and eukaryotes

06

Translation of mRNA

• Genetic code and translation machinery • Stages of translation (initiation, elongation, termination) • Differences between prokaryotic and eukaryotic translation

07

Applications of AI in Molecular Biology

• Introduction to biological databases and AI tools (BLAST, Ensembl, AlphaFold) • Sequence similarity classification • Use of simple AI-based alignment tool • Demonstration of supervised learning algorithm (e.g., decision tree for mutation classification) • RNA and protein structure prediction using online AI tools Not all listed databases and bioinformatics tools use AI.

Unit

Title

Topics Covered

1

Introduction to Engineering Balances

• What is a process? • System and control volume • Steady vs. unsteady processes • Extensive vs. intensive variables • Basic process diagrams (block flow, PFD)

2

Fundamentals of Units and Dimensions

• Dimensional homogeneity • Unit conversion and SI system • Dimensional analysis (Buckingham π-theorem introduction) • Consistency checks in engineering equations

3

Mass Balance without Reactions

• General mass balance equation • Batch, semi-batch, and continuous systems • Steady-state vs. transient processes • Single and multiple unit processes • Recycle, bypass, and purge calculations

4

Mass Balance with Chemical or Biochemical Reactions

• Introduction to reaction stoichiometry • Limiting and excess reactants • Conversion, yield, and selectivity • Mass balances involving microbial growth or enzymatic reactions • Oxygen balance in aerobic fermentation (application)

5

Energy Balance without Reactions

• First law of thermodynamics for closed and open systems • Heat, work, internal energy, enthalpy • Energy balance at steady and unsteady states • Enthalpy calculations: heat capacities, phase changes • Energy balances in mixing, heating, and evaporation

6

Energy Balance with Reactions

• Heat of reaction • Heat of formation and combustion • Energy balances with biochemical reactions (e.g., ATP yield) • Combined mass and energy balance problems

7

Momentum Balance (Introductory)

• Pressure drop in pipes (Bernoulli’s equation and friction losses) • Forces on submerged surfaces • Basic fluid statics and dynamics • Applications to stirred tanks, fermenters, and filtration

8

Applications in Bioprocess Engineering

• Material and energy balances in bioreactors • Case study: batch and fed-batch fermentation • Case study: sterilization, downstream processing • Introduction to process simulation tools (e.g., SuperPro, HYSYS, or Excel modeling)

Tutorial

Title

Key Concepts

Relevance to Bioprocess Engineering

Bioprocess Example

1

Units, Dimensions, and Process Diagrams

• SI units, dimensional homogeneity • Process flow diagrams: batch vs. continuous, upstream vs. downstream

• Essential for fermentation media preparation, sterilization systems, and downstream recovery

• Interpret fermentation + centrifugation process diagram • Perform unit conversions for flowrates (e.g., L/h to m³/s)

2

Mass Balances without Reactions

• General mass balance: input = output • Steady vs. unsteady systems

• Applied to medium prep, nutrient dilution, and buffer prep for batch cultures

• Calculate glucose concentration after dilution • Mass balance in biomass washing step

3

Mass Balances with Recycle, Bypass, and Purge

• Recycle, bypass, and purge streams • Multiple unit systems

• Recycling unconverted substrates or water; purging CO₂ to control contamination

• Analyze fed-batch fermenter with partial substrate recycle • Calculate purge rate in aerobic fermenter

4

Mass Balances with Chemical or Biochemical Reactions

• Reaction stoichiometry • Limiting/excess reactants, conversion, yield, selectivity

• Foundation for microbial growth models, fermentation yield, metabolic design

• Model glucose fermentation to ethanol • Compute biomass yield and oxygen uptake rates

5

Energy Balances without Reaction

• First Law for closed/open systems • Sensible heat, latent heat, heat exchangers

• Estimate energy for sterilization, bioreactor heating, solvent evaporation

• Calculate energy to heat 500 L of media from 25 °C to 121 °C • Estimate steam demand for sterilization

6

Energy Balances with Reactions

• Heat of reaction • Enthalpy of formation • Combined mass-energy balances

• Important for exothermic fermentations, thermophilic processes, anaerobic digestion

• Estimate heat release in aerobic glucose fermentation • Calculate cooling needs for lactic acid production

7

Introduction to Momentum Balances

• Bernoulli equation, pressure drop, friction losses • Fluid statics and pump sizing

• Applies to agitation, air sparging, filtration, and fluid transport in bioreactors

• Calculate pressure drop in membrane filtration • Estimate pump power for recirculation in bioreactor

8

Integrated Case Study: Fermentation and Downstream Processing

• Combined material and energy balances • Multi-step process flow analysis

• Encourages integrated thinking: upstream + heat management + separation efficiency

• Case study: Glucose fermentation → Cell separation → Distillation • Solve for material flows, recycle, energy consumption

Module

Chapter

Title

Topics Covered

Module 1 Foundations of Analytical Methods

1

Introduction to Analytical Chemistry

• Role and scope of analytical chemistry • Qualitative vs. quantitative analysis • Analytical process overview • Classical vs. instrumental methods • Applications in industry, environment, health, food

Module 1 Foundations of Analytical Methods

2

Chemical Measurements and Experimental Error

• Units and chemical quantities • Random, systematic, gross errors • Accuracy, precision, detection/quantification limits • Use of blanks, controls, replicates • Calibration and standardization basics

Module 1 Foundations of Analytical Methods

3

Chemistry of Solutions

• Solvent-solute interactions • Electrolyte and nonelectrolyte solutions • Concentration units (M, m, ppm, %) • Dilution, mixing, ionic strength • Solubility and common ion effect

Module 1 Foundations of Analytical Methods

4

Data Processing and Statistical Analysis

• Significant figures, rounding rules • Mean, SD, relative error • Confidence intervals • Q-test, t-test, F-test • Calibration curves, linear regression

Module 2 Quantitative Chemical Analysis

5

Chemical Equilibria in Analytical Chemistry

• Equilibrium constant K, reaction quotient Q and Gibbs free energy ΔG • Acid-base equilibria, pH, pKa, buffers • Solubility and precipitation equilibria • Complexation and stability constants

Module 2 Quantitative Chemical Analysis

6

Classical Quantitative Methods

• Gravimetric analysis: precipitation, drying • Titrimetric methods: — Acid-base titrations — Redox titrations (KMnO₄, I₂) — Complexometric titrations (EDTA) — Precipitation titrations • Indicators and endpoints • Analyte concentration calculations

Module 3 Electrochemical & Spectroscopic Methods

7

Electrochemical Analysis

• Electrochemistry fundamentals • Electrode potentials, Nernst equation • Potentiometry: pH meters, ISEs • Conductometry • Redox titrations, coulometry • Intro to voltammetry, amperometry

Module 3 Electrochemical & Spectroscopic Methods

8

Molecular and Atomic Spectroscopy

• Molecular: UV-Vis spectrophotometry, fluorimetry (optional) • Atomic: AAS, AES, ICP • Beer-Lambert Law • Calibration curves • Instrumentation and maintenance

Module 4 Analytical Separations

9

Separation Techniques and Instrumental Analysis

• Chemical separation principles • Liquid-liquid extraction • Filtration, centrifugation, membrane methods • Chromatography: Paper, TLC, GC, HPLC, ion-exchange, size-exclusion, affinity • Electrophoresis and capillary electrophoresis • Introduction to mass spectrometry

Week

Focus Topics

Key Activities

Industry & Software Integration

1

Analytical Methods and Errors

• Classify errors (systematic vs. random) • Apply significant figures, % error • Compare methods (e.g., vitamin C in juice)

Nutritional labeling in food industry Tool: ChemCollective Virtual Lab for error simulation

2

Solution Concentrations and Dilutions

• Calculate molarity, ppm, %w/v • Design dilution protocols • Convert units

Reagent prep in QC labs Tool: Dilutions Interactive Tool – ChemCollective

3

Ionic Strength, Solubility, and pH

• Calculate ionic strength • Predict solubility changes • Estimate pH

Formulation of intravenous fluids, fermentation media Tool: PHET pH Simulator

4

Calibration and Statistical Analysis

• Build calibration curve • Apply Q-test, SD, confidence intervals

Pharma: UV-Vis calibration for drug assays Tool: Excel or Desmos Statistics Tool for linear regression

5

Buffer Systems and Acid-Base Equilibria

• Calculate buffer pH & capacity • Use Henderson-Hasselbalch • Compare theoretical vs. actual

Biological buffer prep in enzyme assays Tool: Buffer Maker – OpenWetWare

6

Solubility and Gravimetric Analysis

• Solve Ksp problems • Predict precipitation • Compute gravimetric yield

Trace metal detection in water testing Tool: Virtual Gravimetric Analysis – ChemCollective

7

Titration Methods (Acid-Base, Redox, EDTA)

• Solve titration stoichiometry • Calculate concentrations • Select appropriate indicators

Water hardness analysis, acid content in beverages Tool: Titration Simulator – ChemCollective

8

Electrochemical Analysis

• Use Nernst equation • Analyze pH meter data • Interpret titration curves

pH control in fermentation, ion-selective sensors in environment Tool: Electrochemistry Sim – PHET

9

UV-Vis Spectrophotometry

• Apply Beer-Lambert Law • Build calibration curve • Analyze absorbance data

Protein assays, colorimetric food tests Tool: Spectragryph – Free UV-Vis software

10

Chromatography and Separation

• Calculate Rf • Interpret chromatograms • Compare GC, TLC, HPLC

Pesticide residue analysis, pharma QC Tool: TLC Viewer – ACD Labs (free version)

11

Extraction, Crystallization, and Purification

• Calculate distribution coefficients • Design extraction steps • Predict crystallization

Purification of antibiotics or flavors Tool: Draw & simulate extraction with LibreChem Sketcher

12

Integrated Workflow & Review

• Design full workflow for sample analysis • Peer-review team designs • Solve integrative exam-style problems

Lab validation procedures for food/pharma samples Tool: Use Calc to present a full analytical process (flowchart + calculations)

Week

Focus

Core Activities

Output

1

Project Launch + Experimental Design and Logbook Setup

Safety briefing, team formation, introduction to multi-enzyme production and industrial relevance

Group plan + sampling strategy

2

Sampling

Field collection of soil/rhizosphere samples, metadata recording, sample handling

Environmental sample catalog

3

Media Preparation and Serial Dilution

Preparation of general and selective media (starch, skim milk, CMC, tributyrin), serial dilutions

Plated samples on four selective media

4

Isolation of Bacillus spp.

Heat-shock pretreatment, plating on nutrient agar, streaking for colony isolation

Isolated and purified colonies

5

Screening for Extracellular Enzyme Activities

Plate-based screening: amylase (starch), protease (milk), cellulase (CMC), lipase (tributyrin)

Halo measurements, enzyme profile table

6

Morphological and Microscopic Characterization

Colony morphology, Gram staining, endospore check

Microscopy photographs + isolate descriptions

7

Phenotypic Identification of Selected Isolates

Catalase, oxidase, glucose/lactose fermentation; optional API galleries

Presumptive identification of top strains

8

Growth Optimization Setup

Design pH/temperature/salinity matrix for selected isolates; inoculate starter cultures

Experimental setup log

9

Enzyme Production Under Optimized Conditions

Submerged fermentation; time-point sampling; OD600 measurement

Growth curve + enzyme production chart

10

Enzymatic Quantification (Liquid Assay)

DNSA for amylase, tyrosine release for protease, CMC-reducing sugar for cellulase, etc.

Enzyme activity data table (U/mL)

11

Real-life Application Tests

Run functional tests (e.g., stain removal and dough enhancement, dye decolorization)

Photo/score-based comparison

12

Data Interpretation and Comparative Analysis

Compare enzyme activity profiles, evaluate optimal production conditions, assess strain performance, and discuss potential applications.

Draft result summary + comparison matrix

Step

Title

Activities

Output

Linked Theory / Notes

1

Project Kickoff and Sample Allocation

• Define project goals • Receive brief and broth sample • Identify target analytes (acetic acid, pH, sugars, ethanol, ions) • Assign team roles and tasks

• Team analytical plan (1 page) • Sample intake form

Project design, analyte mapping

2

Sample Pre-treatment

• Filtration • Centrifugation (if turbid) • pH measurement • Aliquoting

• Prepared samples • Baseline pH data

Sample handling, reproducibility

3

Titrimetric Quantification of Acetic Acid

• NaOH titration with indicator or pH meter • Calculation of molarity and mass

• Acetic acid concentration (g/L or % v/v)

Acid-base equilibrium, pKa

4

Redox Titration for Residual Ethanol

• Use dichromate or permanganate • Optional distillation • Redox stoichiometry

• Ethanol content (qualitative or quantitative)

Redox reactions, fermentation products

5

EDTA Titration for Metal Ions (optional)

• EDTA titration with Eriochrome Black T • Target: Ca²⁺, Mg²⁺

• Water hardness or ion concentration (mg/L)

Complexometric titration

6

Gravimetric Analysis of Residual Salts

• Precipitate sulfate or chloride • Filter, dry, weigh • Back-calculate

• Mass and % of target ion

Solubility, gravimetric principles

7

UV-Vis Spectrophotometric Analysis of Reducing Sugars

• Use DNSA or Benedict’s reagent • Build glucose standard curve • Apply Beer-Lambert Law

• Sugar concentration (mg/L or %)

Beer-Lambert Law, reducing sugars

8

Qualitative Analysis by TLC

• Run TLC with standards • Visualize (iodine/UV) • Calculate Rf values

• Identified compounds • Chromatogram image

Chromatography principles

9

Quality Control and Recovery Validation

• Spike-recovery tests • Blank and replicate trials • % Recovery and RSD

• QC sheet with recovery rates

Analytical accuracy and precision

10

Final Data Processing and Interpretation

• Compile all data • Identify key correlations • Compare to references

• Draft tables and figures

Data analysis, literature comparison

11

Final Report & Presentation

• Write group report • Present (poster or oral) • Peer and instructor feedback

• Final project grade

Scientific communication, teamwork

Chapter

Title

Key Topics

1

Fundamentals of Thermodynamics

• Thermodynamic systems and surroundings• State variables and state functions (U, H, S, G)• First and Second Laws of Thermodynamics• Thermodynamic equilibrium and reversibility

2

Gibbs Free Energy and Chemical Equilibrium

• Gibbs free energy (ΔG, ΔG°′)• Enthalpy, entropy, and spontaneity• Equilibrium constant and reaction direction• Reaction coupling and energy transduction

3

Bioenergetics and Biological Energy Transformations

• ATP as the cellular energy currency• High-energy phosphate compounds• Energy coupling in biological systems• Biological energy transformations

4

Redox Thermodynamics and Microbial Energy Metabolism

• Oxidation-reduction reactions and redox potential• Electron carriers and electron transport chains• Aerobic and anaerobic energy metabolism

5

Thermodynamics of Microbial Growth and Bioconversion

• Energetics of microbial growth• Biomass formation and substrate utilization• Thermodynamic constraints on microbial metabolism• Energy efficiency in fermentation

6

Thermodynamics of Biocatalysis and Industrial Bioprocesses

• Thermodynamics of enzyme-catalyzed reactions• Thermodynamic feasibility of bioprocesses• Energy considerations in industrial biotechnology• Case studies in bioprocess optimization

Tutorial

Title

Focus

1

Thermodynamic Fundamentals

Thermodynamic systems, state variables, and the First and Second Laws of Thermodynamics

2

Gibbs Free Energy and Chemical Equilibrium

Gibbs free energy, spontaneity, equilibrium constants, and reaction coupling

3

Bioenergetics

ATP, biological energy transformations, and energy coupling

4

Redox Thermodynamics

Redox reactions, electron carriers, and microbial energy metabolism

5

Microbial Growth Energetics

Biomass yield, substrate utilization, and thermodynamic constraints on microbial growth

6

Thermodynamics of Bioprocesses

Energy efficiency, fermentation energetics, and industrial bioprocess applications

7

Integrated Problem Solving

Application of thermodynamic principles to microbial and enzymatic systems

8

Course Review and Case Studies

Integration of thermodynamic concepts through biotechnology case studies

Unit

Title

Key Topics

1

What Is Engineering?

• Definitions and engineering approach to problem-solving • Differences between science, technology, and engineering • Engineering disciplines in the 21st century • The engineer’s responsibility to society

2

The Role of the Enzyme and Bioprocess Engineer

• Functions of enzyme and bioprocess engineers • Industrial sectors: food, pharma, bioenergy, environment • Real-world examples and case studies • Guest talk or documentary review (optional)

3

Becoming an Engineer: Mindset and Tools

• Systems thinking and process design • Innovation and creativity under constraint • Modern engineering tools (sketching, modeling, project planning) • Engineering habits: curiosity, rigor, resilience

4

Enzyme Engineering Curriculum Roadmap

• Structure of the 3-year specialization • Key concepts and competencies by semester • Integration of science and engineering modules • Personal academic trajectory planning

5

Ethics, Responsibility, and Sustainability

• Codes of ethics for engineers • Engineering and the UN Sustainable Development Goals (SDGs) • Case study: enzyme use in sustainable processing • Personal ethics in research and industry

6

Professional Skills and Career Development

• Types of engineering roles: R&D, production, quality, regulatory, entrepreneurship • Technical communication: reports, presentations, teamwork • Job market overview, internships, professional networking • Building a personal development plan

7

Industrial Careers of Enzyme Engineers

• Research and Development (R&D) • Process and Production • Application Engineering / Technical Support • Formulation and Product Development • Quality and Regulatory Affairs • Business, Sales, and Strategy • Innovation and Entrepreneurship

8

Working with Other Engineers in Industry

• Engineering team structures in bioprocess industries • Roles of mechanical, electrical, automation, environmental, and quality engineers • Cross-functional collaboration examples (e.g., fermenter installation, scale-up) • Communication skills and team dynamics

10

Personal Project: “My Path as an Engineer”

• Guided reflection on values, goals, and motivations • Mapping future career path • Drafting an engineering identity statement • Oral presentation and peer feedback

Session

Scientific Theme

Activities

Language Focus

1

Introduction to Scientific Communication

• Icebreakers • Introduction to yourself as a science student

Vocabulary: academic introductions (studies, goals) Grammar: present simple ("I study", "I am interested in...") Function: introducing oneself

2

Basics of Biological Systems

• Key vocabulary of cells, DNA, enzymes • Pronunciation practice

Vocabulary: basic biology terms Grammar: nouns and adjectives ("cellular structure", "genetic material") Function: describing concepts

3

Scientific Listening Practice 1: Life Sciences

• Watch TED-Ed/BBC clip • Listening for gist and key words

Listening Skills: identifying main ideas Vocabulary: life sciences terms Grammar: past simple for discoveries

4

Talking About Biological Processes

• Describe a simple biological process (photosynthesis, fermentation)

Vocabulary: verbs of processes ("absorb", "convert", "release") Grammar: passive voice ("Glucose is produced by...") Function: describing mechanisms

5

Scientific Listening Practice 2: Bioengineering Innovations

• Listen to a short innovation story • Summarize and discuss

Listening Skills: recognizing technical terms Vocabulary: biotechnology and innovation Grammar: modal verbs ("can", "could")

6

Functional English: Asking and Explaining in Science

• Practice asking for clarification • Practice giving simple scientific explanations

Vocabulary: explaining (e.g., "This means that...") Grammar: question forms ("What does it do?", "How does it work?") Function: clarifying and explaining

7

Mini Presentation 1: Simple Biological Concept

• Prepare and deliver a 2-minute talk on a biological term/process

Vocabulary: process words ("grow", "transform") Grammar: linking words ("first", "then", "finally") Function: presenting ideas clearly

8

Talking About Scientific Data

• Describe simple graphs, tables, experimental results

Vocabulary: describing trends ("increase", "decrease", "stable") Grammar: comparatives and superlatives ("higher", "more significant") Function: interpreting data

9

Scientific Listening Practice 3: Environmental Applications

• Listen to a short talk (e.g., biofuels, sustainability) • Extract main arguments

Listening Skills: listening for argumentation Vocabulary: environment, green technologies Grammar: cause and effect ("due to", "as a result")

10

Mini Presentation 2: Scientific News Summary

• Present a recent scientific news story (chosen with teacher help)

Vocabulary: news reporting ("recently discovered", "researchers found") Grammar: past tenses, reported speech

11

Final Preparation Workshop

• Practice presentation skills • Pronunciation, flow, linking phrases

Vocabulary: transition words ("however", "moreover") Grammar: complex sentences for argumentation Function: organizing a talk

12

Final Speaking Task

• Final oral exam: individual presentation on a simple bioengineering topic + Q&A

Evaluation of: fluency, vocabulary range, structure, pronunciation, scientific clarity

Chapter

Title

Key Topics

1

Introduction to Heat and Mass Transfer in Bioprocesses

• Importance of transport phenomena in enzyme and microbial processes • Applications in bioprocess engineering and bioseparations • Relationship with thermodynamics and macroscopic balances • Role in bioreactor and process design

2

Heat Transfer Mechanisms

• Modes of heat transfer: conduction, convection, and radiation • Thermal properties of materials (thermal conductivity, thermal diffusivity, specific heat) • Heat transfer in biological materials and fluids • Thermal resistance concept

3

Conduction Heat Transfer

• Fourier's Law • Steady-state one-dimensional conduction (plane wall, cylinder, sphere) • Composite walls and insulation • Unsteady-state conduction (lumped capacitance model)

4

Convective Heat Transfer

• Newton's Law of Cooling • Natural and forced convection • Dimensionless numbers (Reynolds, Prandtl, Nusselt) • Heat transfer correlations • Applications in bioreactors and cooling systems

5

Heat Exchangers for Bioprocessing

• Types of heat exchangers (shell-and-tube, plate, double-pipe) • Overall heat transfer coefficient (U) • Log Mean Temperature Difference (LMTD) method • Effectiveness–NTU method • Applications in media sterilization and fermentation temperature control

6

Fundamentals of Mass Transfer

• Molecular diffusion and convective mass transfer • Fick's First and Second Laws • Diffusion coefficients • Analogies between heat and mass transfer

7

Convective Mass Transfer

• Film theory and mass transfer resistance • Mass transfer coefficients • Dimensionless numbers (Sherwood, Schmidt, Reynolds) • Applications in gas–liquid and solid–liquid systems

8

Mass Transfer in Bioprocess Equipment

• Gas–liquid mass transfer principles • Oxygen transfer in fermenters (kLa, aeration, agitation) • Membrane processes (ultrafiltration, nanofiltration, reverse osmosis) • Solid–liquid extraction and enzyme recovery • Transfer limitations during scale-up

9

Heat and Mass Transfer in Bioprocess Unit Operations

• Drying of enzymes, biomass, and probiotics • Freeze-drying and spray drying • Evaporation and moisture diffusion • Heat and mass transfer considerations in sterilization and Clean-in-Place (CIP) systems

Tutorial

Focus

Activities

Bioprocess Relevance

1

Introduction & Application Mapping

• Brainstorm heat/mass transfer in bioprocesses • Annotate a process diagram (fermenter or spray dryer)

Activates prior knowledge and links to real processes

2

Steady-State Conduction in Fermenter Walls

• Calculate heat loss through metal and insulation • Compare insulation materials

Common issue in fermenter and tank design

3

Unsteady Conduction & Enzyme Thermal Inactivation

• Model transient heating of enzyme solution • Relate to enzyme denaturation curves

Critical for enzyme storage and thermal processing

4

Forced Convection in Bioreactors

• Calculate convective heat transfer coefficient (h) • Compare cooling jacket vs. internal coil designs

Essential for bioreactor temperature control

5

Heat Exchanger Sizing

• Design a plate heat exchanger • Compare parallel vs. counter-current flows

Sterilization systems and medium cooling

6

Diffusion Through Biological Membranes

• Calculate glucose diffusion across a dialysis membrane • Estimate equilibrium time

Applications in cell encapsulation and immobilization

7

Oxygen Transfer in Fermenters

• Estimate kLa • Balance oxygen supply with microbial demand

Core mass transfer challenge in aerobic fermentations

8

Mass Transfer in Immobilized Enzymes

• Estimate diffusion resistance in porous matrices • Compare internal and external mass transfer effects

Key to enzyme reactor design and process yield

9

Convective Mass Transfer & Extraction

• Analyze aqueous extraction of amylase • Optimize agitation conditions

Recovery of bioactive compounds and enzymes

10

Heat and Mass Transfer in Drying

• Estimate drying time for enzyme powders • Discuss factors affecting enzyme stability

Enzyme powder production and probiotic drying

11

Case Study: Process Optimization

• Analyze failure or inefficiency (e.g., spray drying or cooling loop) • Propose design improvements

Realistic problem-solving and cost reduction in industry

12

Exam Prep & Wrap-Up

• Mixed mini-problems (diffusion, exchanger, drying) • Consolidation and Q&A

Reinforcement of core concepts for final assessment

Chapter

Title

Key Topics

Bioengineering Examples

1

Introduction to Design of Experiments

• Principles and objectives of DoE • Experimental variables and responses • Experimental error, replication, randomization, and blocking • One-factor-at-a-time (OFAT) versus DoE • Introduction to ANOVA

• Evaluating the effect of pH on enzyme activity • Comparing microbial strains for enzyme production

2

Factorial Experimental Designs

• Full factorial designs • Main effects and interaction effects • Fractional factorial designs • Confounding and design resolution • Screening designs (Plackett–Burman)

• Screening fermentation parameters affecting enzyme production • Identifying critical factors in bioprocess optimization

3

Response Surface Methodology and Process Optimization

• Response Surface Methodology (RSM) • Central Composite Design (CCD) • Box–Behnken Design (BBD) • Regression models • Response optimization and desirability functions • Model validation

• Optimizing enzyme production conditions • Optimizing microbial fermentation media and operating conditions

4

Advanced Experimental Designs and Industrial Applications

• Mixture designs • Split-plot and nested designs (overview) • Robust process design (Taguchi methods) • Industrial applications of DoE • Introduction to statistical software (R, Design-Expert, JMP, Minitab)

• Optimizing enzyme formulations • Scale-up studies and industrial bioprocess optimization

Element

Details

Project Title

Design and Optimization of Enzyme Production Using Experimental Design Methods

Objective

Apply the complete Design of Experiments (DoE) cycle — from single-factor analysis to advanced optimization — to improve α-amylase production by a microbial or fungal strain. Students will work in teams to design, conduct, analyze, and present their experimental project.

Deliverables

• Experimental results (all phases) • Data analysis reports (Excel or R outputs) • Group oral presentation • Written final project report

Project Timeline

6 lab sessions (3h each)

Session

Focus

Activities

Expected Outputs

Lab 1

Introduction and Single-Factor Experiment

• Choose a key variable (e.g., temperature, pH, carbon source) • Perform a One-Variable-At-a-Time (OVAT) study • Plot enzyme activity vs. variable

• OVAT graph • Identification of trends and initial hypotheses

Lab 2

Full Factorial Design (2² or 2³)

• Choose 2 or 3 major factors • Build a full factorial matrix • Run experiments • Create main effects and interaction plots

• Factorial design data • Main effects and interactions interpretation

Lab 3

Screening Designs (Plackett–Burman)

• Apply Plackett-Burman design • Screen several medium components (e.g., nitrogen source, salts, minerals) • Conduct basic statistical analysis

• Identification of most influential factors • Recommendation for optimization study

Lab 4

Response Surface Design (CCD or BBD)

• Use 2–3 key factors to design CCD or BBD experiments • Collect response data • Analyze using R (rsm package) or Design-Expert

• Response surface model • Contour and 3D plots • Optimization results

Lab 5

Model Validation and Residual Analysis

• Conduct confirmation experiments • Analyze residuals and model fit (normality, homoscedasticity) • Calculate R², adj R², PRESS, etc.

• Model validation report • Final optimized conditions identified

Lab 6

Final Report and Presentation

• Prepare and present scientific poster or oral talk • Defend design choices, results, and optimization strategy • Peer review between groups

• Final presentation (slides or poster) • Final written report (structured like a scientific article: intro, methods, results, discussion)

Chapter

Title

Key Topics

1

Introduction to Immobilization

• Importance in industrial and environmental biotechnology • Free vs. immobilized systems: advantages and limitations • Overview of immobilized biocatalysts (enzymes and cells)

2

Methods of Immobilization

• Physical immobilization methods • Chemical immobilization methods • Combined immobilization strategies • Selection of appropriate immobilization methods

3

Supports and Carriers

• Classification of support materials (organic, inorganic, and synthetic) • Physicochemical properties of supports • Selection criteria for immobilization supports

4

Kinetics and Mass Transfer in Immobilized Systems

5

Immobilization of Microbial Cells

• Benefits of whole-cell immobilization • Comparison: immobilized cells vs. free cells • Entrapment and encapsulation techniques • Industrial applications: ethanol production, bioremediation

6

Bioreactor Design and Integration

• Types of immobilized bioreactors (batch, packed-bed, fluidized-bed, membrane) • Residence time and reactor selection • Operational stability and biocatalyst reuse • Scale-up strategies and productivity evaluation • Process integration and downstream processing

7

Industrial Applications and Case Studies

• Glucose isomerization with immobilized glucose isomerase • Bioethanol production using immobilized yeast • Dye decolorization using immobilized laccase • Emerging trends: biosensors, nanocarriers, 3D supports

Element

Details

Mini-Project Title

Comparative Design, Immobilization, and Evaluation of Enzyme Systems Using Physical and Chemical Methods

Enzyme/System

Chosen by Course Coordination Committee (e.g., α-amylase, lipase, laccase, yeast cells).

Deliverables

• Experimental data (for each immobilization method) • Comparative data analysis • Group scientific poster and oral presentation • Written mini-project report

Session

Focus

Activities

Expected Outputs

1

Introduction & Preparation of Immobilization Systems

• Introduction to physical vs. chemical immobilization • Prepare immobilized enzyme samples using: – Adsorption – Entrapment (e.g., alginate beads) – Microencapsulation (liposomes) – CLEAs (Cross-Linked Enzyme Aggregates)

• Four immobilization methods are available. Each team selects one method to study throughout the mini-project, based on a random draw.

2

Immobilization Yield and Initial Activity Assay

• Assay immobilized vs. free enzyme activity • Calculate immobilization efficiency (%) • Analyze reproducibility (triplicates)

• Immobilization yield table • Initial activity comparison graphs

3

Kinetic Behavior: Substrate Affinity (Km, Vmax)

• Perform kinetic assays for each immobilization method • Determine apparent Km and Vmax values • Plot Lineweaver–Burk or nonlinear fits

• Km and Vmax for free vs. each immobilized form • Interpretation of kinetic modifications

4

Operational Stability and Reusability

• Perform repeated batch reactions (reusability test) • Measure and plot residual activity after each cycle • Discuss enzyme leakage or loss of activity

• Reusability curves for each method • Comparison of operational stability

5

Mass Transfer and Microenvironment Effects

• Study agitation speed or bead/matrix type impact • Estimate diffusional limitations • Discuss microenvironment effects (liposomes, CLEAs)

• Activity vs. mixing speed or vs. matrix type • Hypotheses on steric and diffusional limitations

6

Comparative Analysis, Report Writing & Presentations

• Summarize and compare all methods (advantages/limitations) • Prepare and present scientific poster or oral talk • Submit a scientific-style written report

• Final comparative table and conclusions • Oral/poster presentation delivered • Final mini-project report submitted

Chapter

Title

Key Topics

1

Introduction to Microbial Genetics

• Importance and historical milestones • Overview of bacterial, archaeal, and eukaryotic microbial genomes

2

Bacterial Genome Organization

• Chromosomal structure and topology • Plasmids: structure, classification, replication, and properties • Mobile genetic elements: – Transposons (types, mechanisms: replicative vs. conservative) – Integrons (structure, gene cassettes, origins) • Gene arrangement and operon structure

3

DNA Replication, Mutation, and Repair in Bacteria

• Mechanism of DNA replication • Types and consequences of mutations • Mutagenic agents and mutation detection methods • DNA repair mechanisms: direct repair, excision repair, mismatch repair, SOS response

4

Horizontal Gene Transfer (HGT)

• Transformation: natural and artificial competence • Conjugation: F plasmids, Hfr strains • Transduction: generalized and specialized • Genetic mapping and recombination analysis

5

Gene Expression and Regulation

• Transcription and translation mechanisms • Regulation models: lac and trp operons • Attenuation and anti-termination • Epigenetic regulation and regulatory RNAs • Sequence inversion and regulatory switches

6

Yeast Genetics as a Model System

• Biology and culture of Saccharomyces cerevisiae • Genome, transcriptome, and proteome overview • Genetic manipulation: gene knockout, tetrad analysis • Complementation and gene conversion • Mitochondrial genetics in yeast

7

Archaea: Diversity and Genetics

• General features and ecological roles • Archaeal genome organization and DNA replication • Gene expression mechanisms in archaea • Archaea of Asgård: evolutionary insights

8

Genetic Tools and Applications in Biotechnology

• Applications of plasmids, transposons, and integrative elements • CRISPR-Cas systems for genome editing • Synthetic biology and regulatory circuits • Case studies: microbial strain improvement in biotechnology

Tutorial

Focus

Activities

Skills Developed

1

Introduction to Microbial Genomes

• Compare bacterial, archaeal, and yeast genomes (size, structure, features) • Match genome types to specific environmental adaptations

• Data interpretation • Genome structure understanding

2

Operons and Gene Organization

• Analyze operon maps (e.g., lac operon, trp operon) • Predict gene expression outcomes upon different mutations

• Operon analysis • Regulatory logic reasoning

3

Mobile Genetic Elements

• Solve case studies on transposon insertions and their consequences • Identify effects of mobile elements on gene regulation and genome evolution

• Problem-solving • Genetic consequence prediction

4

Mutation Types and Repair Mechanisms

• Classify mutations from given DNA sequences • Match DNA lesions to appropriate repair pathways (direct, mismatch, excision, SOS)

• Mutation analysis • Repair strategy identification

5

Horizontal Gene Transfer Mechanisms

• Analyze transformation, conjugation, and transduction experimental designs • Predict outcomes of gene transfer experiments

• Understanding HGT mechanisms • Critical thinking on gene mobility

6

Gene Regulation Beyond Operons

• Solve problems on attenuation and anti-termination (e.g., trp operon control) • Analyze hypothetical regulatory RNA sequences (riboswitches, sRNAs)

• Advanced transcription regulation • RNA-based control mechanisms

7

Yeast Genetics and Tetrad Analysis

• Practice tetrad dissection results interpretation (linkage analysis) • Solve complementation tests and gene conversion problems

• Classical genetic mapping • Application of yeast as a model

8

Archaeal Genetics

• Comparative questions: bacteria vs. archaea replication and transcription • Analyze gene expression pathways in extremophiles

• Evolutionary and functional analysis

9

CRISPR-Cas and Genome Editing

• Design a simple CRISPR-Cas experiment (guide RNA, Cas type, editing strategy) • Analyze off-target effects and discuss ethical implications

• Practical genome editing understanding • Ethical reflection

10

Applications of Microbial Genetics in Biotechnology

• Case studies: improving a microbial strain for ethanol production or enzyme secretion • Design a basic strain improvement workflow

• Application of genetics to real-world problems • Experimental design thinking

Session

Title

Key Activities

1

Workshop Introduction: Project Plan, Biosafety, Buffer Preparation

• Project overview and biosafety • Preparation of basic buffers and solutions

2

Genomic DNA Extraction (Salting-Out Method)

• Extraction using salting-out • Purity assessment (A260/A280)

3

Genomic DNA Extraction (Spin-Column Method) and Method Comparison

• Extraction using spin-column • Yield/purity comparison with salting-out

4

PCR Principles, Primer Selection, and Reaction Setup

• Principles of PCR and primer selection • Preparation of the PCR reaction mixture for 16S rRNA and α-amylase genes • Selection and preparation of positive and negative controls • Good PCR laboratory practices (contamination prevention, sterile pipetting, use of filter tips)

5

PCR Execution and Troubleshooting

• Run PCR • Immediate first troubleshooting if problems occur

6

Agarose Gel Electrophoresis and Gel Documentation

• Run gels • Document bands • Band size estimation

7

PCR Product Cleanup and Sequencing Preparation

• Cleanup (exonuclease/SAP or kits) • Prepare samples for sequencing

8

Introduction to qPCR Applications (Theory Session)

• Short introduction to qPCR principles and industrial/research applications

9

Bioinformatics I: Sequence Quality Assessment, BLAST, and Sequence Alignment

• Assess sequence quality and trim low-quality regions (overview) • Export sequences in FASTA format • Perform BLAST searches against the NCBI database • Retrieve homologous sequences • Perform basic multiple sequence alignment

10

Bioinformatics II: Phylogenetic Tree Construction and Sequence Quality Assessment

• Review sequence quality and chromatograms • Construct a phylogenetic tree (Neighbor-Joining) • Interpret evolutionary relationships and confirm microbial identification

11

Report Writing Workshop

• How to structure the report • Data presentation (figures, tables, legends) • Bibliography formatting (e.g., Zotero)

12

Student Oral Presentations and Peer Feedback

• Students present findings orally • Peer and instructor feedback

Session

Title

Key Activities

Expected Output

1

Workshop Introduction and Biomass Collection

• Introduction to workshop objectives and biosafety • Visit an agro-industrial facility (or receive supplied residues) • Collect, document, and classify biomass samples

Characterized biomass samples and sampling records

2

Biomass Preparation and Pretreatment Planning

• Drying and grinding biomass • Moisture determination • Selection of appropriate pretreatment strategy based on target material

Prepared biomass and pretreatment plan

3

Biomass Pretreatment and Fractionation

• Alkaline, acid, or enzymatic pretreatment • Separation of cellulose, hemicellulose, lignin, or starch fractions • Recovery and washing of fractions

Pretreated biomass fractions

4

Project Planning and Team Assignment

• Assignment of project tracks (CNC/CNF, PHB/PHA, TPS, CMC, lignin-based materials, composites) • Experimental planning and workflow design • Preparation of reagents and materials

Project plan and experimental workflow

5

Biomaterial Production – Phase I

• Begin material-specific production protocols according to the assigned project • Preparation of nanocellulose, bacterial cultures, modified cellulose, or precursor materials

Intermediate biomaterial products

6

Biomaterial Production – Phase II

• Continue extraction or synthesis procedures • Preparation of polymer matrices, blends, or precursor formulations • Process optimization

Biomaterial formulations ready for shaping

7

Material Shaping and Prototype Fabrication

• Film casting, molding, or gel preparation • Drying and curing procedures • Preparation of prototype biomaterials

Biomaterial prototypes

8

Post-Treatment and Sample Conditioning

• Cross-linking or stabilization (when applicable) • Extraction and purification of target biopolymers • Sample conditioning before testing

Conditioned samples for characterization

9

Physicochemical Characterization

• Measure thickness, density, moisture content, water absorption, swelling, transparency, and solubility

Physicochemical characterization data

10

Mechanical Performance and Biodegradability

• Mechanical testing (tensile strength, elongation, flexibility) • Biodegradation assessment • Optional structural characterization (SEM or FTIR if available)

Mechanical and biodegradation results

11

Process Evaluation and Sustainability Assessment

• Calculate material yield and process efficiency • Perform mass balance calculations • Discuss environmental impact and industrial feasibility

Sustainability and process evaluation

12

Final Project Presentation and Scientific Reporting

• Present project results (oral or poster) • Submit final scientific report • Peer discussion and project evaluation

Final report and oral/poster presentation

Chapter

Title

Key Topics

1

Fluids and Flow Behavior in Bioprocess Systems

• Types of fluids in bioprocessing (broths, slurries, gases) • Physical properties: viscosity, density, surface tension, rheology • Fluid statics and hydrostatic pressure in bioreactors • Relevance to liquid storage, sampling ports, and media tanks

2

Conservation of Mass and Mechanical Energy

• Mass continuity and flow rate calculations in pumps and pipelines • Bernoulli’s equation and energy conservation in bioprocess design • Applications: siphoning, flow through sampling probes, pump performance

3

Flow Regimes and Fluid Motion

• Laminar and turbulent flow in bioreactors and piping • Reynolds number and its application to fermentation and flow loops • Velocity profiles in culture media • Newtonian vs. non-Newtonian behavior in broths

4

Momentum Balances and Head Losses in Bioprocessing

• Shell momentum balances and flow mapping in vessels • Friction losses in tubing and stainless steel piping • Minor losses: elbows, valves, spargers, baffles • Case study: pressure drop in a fermentation loop

5

Flow Through Porous Media and Particle Transport

• Flow in packed beds (chromatographic columns, immobilized enzyme reactors) • Filtration: membrane modules, depth filters • Drag force and settling behavior in centrifuges and sedimentation tanks • Application: biomass harvesting and broth clarification

6

Bioprocess Design, Mixing, Instrumentation, and Scale-Up

• Dimensional analysis for geometric and dynamic similarity • Scale-up criteria for stirred bioreactors and fluid systems (constant Reynolds number, power input per unit volume, tip speed) • Agitation and mixing fundamentals: impeller types, mixing patterns, power consumption, and mixing time • Flow measurement and process instrumentation: rotameters, differential pressure devices, electromagnetic and Coriolis flow meters • Design considerations for pilot- and industrial-scale bioprocesses

Tutorial

Title

Key Activities

1

Fluid Property Estimation in Fermentation Broths

• Calculate viscosity, density, and surface tension for typical broths • Compare Newtonian and non-Newtonian behaviors

2

Hydrostatics in Bioreactors and Media Tanks

• Apply hydrostatic pressure equations • Calculate pressures at sampling ports and tank bottoms

3

Mass Flow and Velocity Through Bioprocess Tubing

• Calculate mass and volumetric flow rates • Relate flow velocity to tube diameter and medium properties

4

Bernoulli Applications in Pump-Sampling Systems

• Apply Bernoulli’s equation • Solve siphoning problems and flow through sampling devices

5

Reynolds Number Calculations for Fermentation Piping

• Calculate Reynolds numbers • Identify laminar vs. turbulent flow in fermenters and pipe networks

6

Velocity Profiles for Glucose and Biomass Flow in Reactors

• Plot and interpret velocity profiles for broth components • Understand implications for mass transfer and mixing

7

Pressure Drop and Head Loss in Recirculation Loops

• Calculate head loss due to friction and fittings • Analyze real-world examples from fermentation circuits

8

Darcy’s Law and Permeability in Filtration Membranes

• Apply Darcy’s law to membrane and depth filtration • Calculate membrane permeability and fouling tendencies

9

Settling Velocity of Microbial Biomass

• Apply Stokes' law to microbial particles • Estimate sedimentation rates in clarifiers and centrifuges

10

Dimensional Analysis: Bioreactor Scale-Up

• Apply Buckingham π-theorem • Derive dimensionless groups relevant to scale-up (e.g., Reynolds, Froude, Weber numbers)

11

Empirical Flow Correlations and Data Fitting for Biological Fluids

• Fit experimental data to flow models • Analyze correlations for non-Newtonian bioprocess fluids

12

Integrated Case Study: Momentum Transfer in a Bioreactor-Separation System

• Solve a complex problem combining fermentation flow, recirculation, and biomass harvesting • Discuss design improvements and troubleshooting

Session

Title

Key Activities and Content

1

Introduction to Bio-Innovation

Definition of bio-innovation; innovation in enzyme engineering, diagnostics, food, health, agriculture, and biocatalysis; difference between scientific discovery and innovation.

2

Emerging Innovations in Biotechnology and Enzyme Engineering

Industrial enzymes, green chemistry, sustainable food processing, enzyme-based diagnostics, biosensors, and biocatalysis; examples of current applications.

3

From Research to Application

Technology Readiness Levels (TRLs), proof of concept, prototype, scale-up, technical feasibility, and the limits of laboratory results.

4

Case Studies in Biotechnology Innovation

Analysis of successful enzyme-related products or companies, such as industrial enzymes, diagnostic kits, food-processing enzymes, or local biotech initiatives.

5

Intellectual Property and Technology Transfer

Patents, protection of enzyme-related inventions, university technology transfer, licensing, spin-offs, and collaboration with industry.

6

Regulation and Certification

Basic regulatory pathways for food enzymes, diagnostic enzymes, industrial enzymes, safety, quality control, and certification requirements.

7

Innovation Ecosystem and Support Structures

• The biotechnology innovation ecosystem: universities, research centers, industry, and government • Innovation support structures: incubators, accelerators, science parks, and technology transfer offices (TTOs) • Funding mechanisms: research grants, seed funding, angel investors, venture capital, startup competitions, and public innovation programs • University–industry partnerships and collaborative research • Commercialization pathways: licensing, spin-offs, and startup creation

8

Mini-Project Workshop: Designing a Bio-Innovation Concept

• Identify a real-world problem or unmet need in biotechnology, food, health, agriculture, or environmental sectors • Identify the main stakeholders and potential end users • Develop an enzyme- or biotechnology-based solution using basic Design Thinking principles • Define the scientific basis, expected benefits, technical feasibility, and value proposition of the innovation

9

Project Coaching and Innovation Validation

• Present the proposed innovation concept for peer and instructor feedback • Evaluate market need and potential users (customer discovery) • Discuss technical feasibility, intellectual property, regulatory considerations, and commercialization pathways • Refine the innovation concept based on feedback

10

Innovation Pitch

Short presentation of the bio-innovation concept: problem, enzyme-based solution, scientific basis, application, feasibility, and valorisation potential.

Unit

Title

Detailed Topics

1

Pollution and Industrial Environmental Impacts

- Types of Pollution: air, water, soil, hazardous waste. - Industrial sources of pollution: manufacturing, mining, energy, agriculture. - Pollution and ecosystem health: basic concepts (eutrophication, acid rain, GHG emissions). - Why Redesign Industries: environmental degradation, resource depletion, global risks. - Role of Industrial Ecology: closing loops, preventing waste, redesigning industrial metabolism.

2

Introduction to Industrial Ecology

- Definitions and history - From linear to circular systems - IE as "the science of sustainability"

3

Systems Thinking and Metabolism of Industry

- Material and energy flows - Urban metabolism vs industrial metabolism - Case studies: urban ecosystems, industrial parks

4

Tools and Methods of Industrial Ecology

- Life Cycle Assessment (LCA): concepts and basics - Material Flow Analysis (MFA) - Emergy and exergy analysis

5

Life Cycle Thinking and Environmental Assessment

- Goal and scope definition - Inventory analysis - Impact assessment (carbon footprint, water footprint) - Interpretation and limitations

6

Industrial Symbiosis and Eco-Industrial Parks

- Concept of industrial symbiosis - Examples: Kalundborg (Denmark), EcoParks worldwide - Designing symbiotic networks

7

Circular Economy and Sustainable Business Models

- Circular economy principles - Product-service systems - Biomimicry and cradle-to-cradle design - Critical discussion: circularity myths and realities

8

Case Studies and Applications

- Application to agri-food industries - Application to biotechnology and biorefineries - Application to construction and manufacturing

9

Policy, Regulation, and Future Trends

- Environmental policies supporting IE (e.g., EU Green Deal, Extended Producer Responsibility) - Future of Industrial Ecology: digital twins, AI in sustainability- Challenges and opportunities

Chapter

Title

Key Topics

1

Introduction

• What is enzyme engineering? • From agriculture to industry: Agro-food processes • The agro-food industry market in Algeria • Health and regulatory aspects of enzyme use • The food enzyme market

2

Industrial Enzyme Production

• Origins of industrial enzymes • Strain development • Fermentation • Downstream processing

3

Endogenous Enzymes, Their Role in Food Product Development

• Definition of Endogenous Enzymes • Role of Endogenous Enzymes in Food Processing • Manipulation of Endogenous Enzymes • Challenges and Opportunities in the Use of Endogenous • Enzymes

4

Industrial Enzymes, Their Role in Food Product Development

• Dairy industry • Baking • Non-wheat-based foods • Starch transformation • Fish product processing • Meat processing • Juice industry • Olive oil industry • Flavor industry

5

Enzymes in Agriculture

• Enzyme applications for soil improvement and bioremediation. • Enzyme-based biopesticides: microbial enzymes for pest control. • Enzyme applications in plant growth: improving nutrient uptake, plant cell wall degradation, and fungal growth management. • Biodegradation of agricultural waste: use of enzymes in waste-to-value applications. • Use of enzymes in composting and organic waste recycling.

6

Enzymes in Animal Feed

• Enzyme supplements in animal feed: improving protein digestibility and nutrient availability. • Cellulases and xylanases in fiber degradation. • Phytases for phosphorus release. • Use of proteases for enhancing animal growth rates. • Cost-benefit analysis of enzyme supplementation in animal feed production.

Session

Title

Industry Focus

Key Learning Focus

1

Enzymatic Browning in Fresh-Cut Fruits and Vegetables

Fresh Produce Industry

Control of endogenous enzymes (PPO), enzymatic browning mechanisms, and solution strategies.

2

Breaking Down Lactose, Building Up Quality: Enzyme Innovations at Milky Way

Dairy Industry

Enzymatic hydrolysis of lactose, industrial lactase application, sensory and regulatory challenges.

3

Enhancing Industrial Couscous Production with Enzyme Innovations

Industrial Cereal (Couscous) Production

Improving texture, hydration, and nutritional value of couscous using enzyme technologies.

4

Sustainable Valorization of Agro-Industrial Waste for IMOs Production

Functional Food Ingredients / Circular Economy

Enzymatic conversion of waste to prebiotic oligosaccharides, sustainable process design.

5

Designing an Enzyme-Based Strategy for Tomato Crop Protection

Agriculture (Plant Protection)

Development of enzyme-based elicitors or biopesticides to enhance plant defenses or control pathogens.

6

Optimizing Enzymatic Supplements for Poultry Feed Efficiency

Animal Feed Industry

Enzyme supplementation to enhance nutrient absorption and feed conversion efficiency in poultry farming.

Chapter

Title

Topics

1

Introduction to Bioprocess Reactions and Reactors

• Biochemical vs. chemical reactions • Role of reactors in bioproduct manufacture • Classification: enzyme-catalyzed, microbial, mixed cultures • Comparison of chemical reactors vs. bioreactors

2

Stoichiometry and Mole Balances

• Conversion, selectivity, yield • Mole balances in batch, CSTR, and PFR • Application to biochemical reactions • Limiting/reducing substrate concept in bioprocessing Terminology note: a limiting substrate and a reducing substrate are distinct concepts; the source pairs these terms without explanation.

3

Biochemical Reaction Kinetics

• Enzyme kinetics (Michaelis–Menten, competitive inhibition) • Microbial growth kinetics (Monod, substrate/product inhibition) • Biomass–substrate–product relationships (e.g., Luedeking–Piret) • Death kinetics and plasmid instability

4

Design of Ideal Bioreactors

• Design equations for batch, CSTR, and PFR reactors • Reactor sizing and performance evaluation • Space time and space velocity concepts • Graphical methods for reactor design and integration • Multiple reactor configurations (series and parallel arrangements) • Comparison of reactor performances for bioprocess applications

5

Reversible and Multiple Reactions

• Reversible biocatalysis • Parallel and series reactions in bioconversion • Enhancing selectivity using process configuration (e.g., membrane reactors)

6

Bioreactor Types, Operation, and Scale-Up Principles

• Classification of bioreactors: stirred-tank (STR), airlift, packed-bed, membrane, and photobioreactors • Reactor configuration, mixing, aeration, and oxygen transfer principles • Key operating parameters: temperature, pH, dissolved oxygen, agitation, aeration rate, and residence time • Immobilized enzyme and whole-cell bioreactors • Solid-state fermentation (SSF) systems and operating conditions • Scale-up considerations: maintaining mixing, oxygen transfer, heat removal, and productivity • Criteria for selecting bioreactor type according to organism, product, and process objectives

7

Heterogeneous Bioreactions and Mass Transfer Limitations

• Internal and external mass transfer in biocatalysis • Thiele modulus and effectiveness factor • Strategies to minimize diffusion limitations • Applications in immobilized enzyme systems and biofilms

8

Bioreactor Experimental Methods and Kinetic Data Analysis

• Rate expression identification from batch data • Integral and differential methods • Method of initial rates and excess reactant • Planning kinetic experiments and avoiding artifacts

Tutorial

Title

Focus

Key Activities

1

Mole Balance Foundations

Applying mole balances to batch, CSTR, and PFR

Solve mole balances for biomass production; Compare 90% conversion times; Ethanol fermentation batch exercise

2

Conversion, Yield, and Selectivity

Performance metrics in biochemical processes

Calculate yield coefficients; Analyze trade-off between conversion and selectivity; Citric acid fermentation case

3

Enzyme Kinetics and Inhibition

Michaelis–Menten modeling and inhibition effects

Plot v vs. [S], Lineweaver–Burk, Eadie–Hofstee; Determine Km and Vmax; Glucose oxidase inhibition case

4

Microbial Growth and Product Formation Models

Monod kinetics and Luedeking–Piret model

Fit Monod parameters; Calculate µmax, Ks, maintenance coefficients; E. coli recombinant protein production

5

Reactor Sizing and Design (Batch and CSTR)

Reactor volume calculations and time requirements

Size batch reactor; Compare CSTR vs. batch; Design challenge for lactic acid production

6

PFR Design and Graphical Integration

Reactor sizing using graphical methods

1/–rA vs. XA plot for PFR sizing; Combine CSTR + PFR; Immobilized enzyme system practice (lactose hydrolysis)

7

Parallel and Reversible Bioreactions

Impact on conversion and product selectivity

Analyze parallel reactions in antibiotic synthesis; Conditions for maximum selectivity; Tryptophan production case

8

Immobilized Systems and Diffusion Limitations

External/internal mass transfer effects

Calculate effectiveness factor with Thiele modulus; Impact of particle size; Enzyme bead reactor application

9

Heterogeneous Biocatalysis and Packed Bed Systems

Mass transfer + reaction in porous media

Determine rate under internal limitations; Calculate productivity; Packed bed case for fructose syrup production

10

Data Analysis for Kinetic Parameter Estimation

Rate determination from experimental data

Apply integral and differential methods; Fit enzyme kinetics; Practice non-linear regression setup

11

Design Challenge (Group)

Collaborative case study on reactor selection

Assign bioprocess; Teams propose reactor type, sizing, performance; Class presentation and justification

12

Final Review and Mini-Mock Exam

Concept integration + exam-style problems

Review key equations; Solve mixed questions; Tips on unit conversions and data interpretation

Chapter

Title

Topics

1

Introduction to Omics Sciences and Genome Organization

• Concept and evolution of omics sciences: genomics, transcriptomics, proteomics, metabolomics • Systems biology and integrative analysis • Prokaryotic and eukaryotic genome organization • Chromosome structure and genome architecture • Extrachromosomal DNA: plasmids, mitochondria, chloroplasts • Overview of omics data generation technologies

2

Genome Mapping, Sequencing, and Assembly

• Genetic and physical mapping concepts • Molecular markers: SNPs, SSRs, and molecular signatures • Genome sequencing technologies: Sanger sequencing, NGS, long-read sequencing • Genome assembly principles: reads, contigs, scaffolds • Genome databases and sequence retrieval • Introduction to genome annotation workflows

3

Comparative and Functional Genomics

• Genome comparison and evolutionary analysis • Identification of conserved and variable genomic regions • Orthologs, paralogs, and gene families • Comparative genomics for microbial identification (16S rRNA, whole genome comparison) • Functional annotation and prediction of gene functions • Applications in microbial biotechnology and strain improvement

4

Transcriptomics and Gene Expression Analysis

• Principles of transcriptomics • RNA sequencing (RNA-seq), small RNA sequencing, and microarrays • RT-PCR and qRT-PCR applications • RNA data processing: quality control, normalization, and filtering • Differential gene expression analysis • Gene set enrichment analysis and pathway interpretation

5

Proteomics and Protein Function Analysis

• Objectives and challenges of proteomics • Protein extraction and separation strategies • 2D-PAGE and isoelectric focusing • Mass spectrometry-based proteomics (MALDI-TOF, LC-MS/MS) • Protein identification databases • Protein–protein interactions and protein networks • Applications in enzyme discovery and biotechnology

6

Functional Genomics and Systems Biology

• Linking genes, transcripts, and proteins to biological functions • Forward and reverse genetics • Gene knockout and functional validation strategies • Regulatory networks and pathway analysis • Protein–DNA and protein–protein interactions • Introduction to metabolomics, lipidomics, and metagenomics

7

Multi-Omics Integration and Biological Network Analysis

• Principles of multi-omics integration • Combining genomics, transcriptomics, and proteomics datasets • Biological network reconstruction • Pathway analysis (KEGG, GO enrichment) • Biomarker and molecular signature discovery • Applications in biotechnology and environmental microbiology

8

Artificial Intelligence and Machine Learning in Omics

• Introduction to machine learning concepts for biological data • Data preprocessing and feature selection • Classification and clustering of omics datasets • AI-assisted genome annotation and sequence analysis • Machine learning for transcriptomic pattern recognition • AI applications in protein structure and function prediction • Challenges and limitations of AI in biological sciences

Tutorial

Title

Objective

Activity / Tool

1

Applications of Omics Approaches

Introduce omics approaches through a visual synthesis activity.

Collaborative work: Create a concept map + literature search based on the article How ‘omics technologies can drive plant engineering, ecosystem surveillance, human and animal health.

2

Genome Mapping

Understand the basics of genetic and physical mapping.

Guided worksheet (questions + result interpretation) based on the article A physical map of the papaya genome with integrated genetic map and genome sequence – Qingyi Yu et al., 2009.

3

Transcriptomic and lncRNA Analysis

Introduction to functional transcriptomics and long non-coding RNAs (lncRNA).

Guided worksheet (questions + interpretation) based on the article Genome-wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep – Xu Feng et al., 2018.

4

Functional Analysis with ShinyGO & STRING

Analyze gene sets with GO/KEGG enrichment (ShinyGO) and explore protein interactions (STRING).

Guided worksheet (questions + result interpretation) based on functional annotation exercises.

5

Simplified Multi-Omics Pipeline (Case Study)

Combine RNA-Seq data with ShinyGO, STRING, AlphaFold, and InterPro to build a coherent biological interpretation.

Guided worksheet using either simulated data or a real case study (e.g., plant or animal stress response).

6

AI and Machine Learning for Omics Analysis

Introduction to AI for clustering, gene networks, and deep learning applied to omics data.

Guided worksheet using platforms like Orange or DeepGO, based on the article AI-assisted prediction of gene-disease associations.

Module

Title

Topics

1

Introduction to Bioinformatics and Biological Databases

• Scope and applications of bioinformatics • Biological data types and biological information flow • Major biological databases: NCBI, EBI, GenBank, RefSeq, UniProt, PDB, Ensembl • Sequence identifiers and accession numbers • Biological file formats: FASTA, FASTQ, GFF, GenBank, BED, VCF • Introduction to Linux command line and reproducible bioinformatics workflows

2

Sequence Analysis and Similarity Searching

• Sequence retrieval and database querying • Pairwise sequence alignment (global and local alignment) • Multiple sequence alignment • BLAST algorithms and interpretation • Sequence motifs and conserved domains • Basic sequence quality assessment

3

Genome Annotation and Functional Analysis

• Gene prediction and genome annotation • ORF identification • Functional annotation using GO, KEGG, InterPro, and Pfam • Primer design and PCR simulation • Introduction to genome browsers

4

Comparative Genomics and Molecular Evolution

• Comparative genomics concepts • Orthologs and paralogs • SNPs and genome variation • Genome assembly concepts (reads, contigs, scaffolds) • Phylogenetic inference methods • Molecular evolution and substitution models

5

Structural Bioinformatics and Integrated Bioinformatics Applications

• Protein structure prediction (homology modeling and AI-based prediction) • Protein visualization • Protein function prediction • Protein–ligand and protein–protein interaction databases • Integrated bioinformatics workflow from sequence to biological interpretation • Introduction to bioinformatics applications in genomics, transcriptomics, and proteomics

Tutorial

Title

Focus

1

Biological Databases

Exploring NCBI, GenBank, RefSeq, UniProt, PDB and Ensembl

2

Sequence Retrieval and File Management

Downloading sequences, accession numbers, FASTA, FASTQ, GFF, GenBank formats

3

Similarity Searches with BLAST

BLAST searches and interpretation of sequence similarity

4

Multiple Sequence Alignment

CLUSTAL Omega, MUSCLE, Jalview

5

Primer Design and PCR Simulation

Primer3 and PCR simulation

6

Genome Annotation

Gene prediction and annotation using RAST, GeneMark, InterPro

7

Functional Annotation

GO enrichment, KEGG pathway analysis, Blast2GO

8

Protein Structure Prediction

SWISS-MODEL, AlphaFold and PyMOL

9

Comparative Genomics

Ortholog identification and genome comparison

10

Phylogenetic Analysis

Tree construction and interpretation using MEGA

11

Genome Browsers and Integrated Analysis

UCSC Genome Browser, Ensembl, Geneious (or similar)

12

Capstone Bioinformatics Project

Complete workflow: sequence retrieval → annotation → functional prediction → phylogenetic analysis

Sessions

Title

Focus

1

Laboratory Opening and Safety Recap Introduction to Enzyme Purification Strategies

• Workshop overview and lab safety reminders • Basic principles of enzyme purification • Importance of yield, purity, and specific activity • Overview of purification steps (precipitation, dialysis, chromatography) • Introduction to the Purification Table (yield %, purification fold, specific activity) • Basic statistical treatment of experimental results (mean, standard deviation)

2

Preparation of Solutions and Culture Media

• Buffer preparation, reagent handling, and sterile techniques

3

Production of α-Amylase by Fermentation

• Microbial cultivation and enzyme production

4

Fractional Precipitation with Ammonium Sulfate

• Concentrating and partially purifying α-amylase

5

Removal of Ammonium Sulfate by Dialysis

• Desalting and preparation for chromatography

6

Size-Exclusion Chromatography and Fraction Analysis

• Separation of proteins according to molecular size (gel filtration) • Collection of eluted fractions • Measurement of protein absorbance at 280 nm (A280) • Identification of protein-containing and enzymatically active fractions • Pooling of active fractions for subsequent purification steps

7

Affinity Chromatography and Fraction Analysis

• Purification based on specific ligand–protein binding interactions • Column equilibration • Sample loading • Washing to remove unbound proteins • Elution of the target enzyme • Collection of eluted fractions • Measurement of protein absorbance at 280 nm (A280) • Identification of enzymatically active fractions • Pooling of active fractions for enzyme characterization

8

Evaluation of Purification

• Construction of purification table: yield, purity, specific activity • Introduction to simple statistical analysis: calculate mean, standard deviation for replicated assays

9

SDS-PAGE and Zymogram Analysis

• Electrophoretic analysis of protein purity • Detection of enzymatic activity (zymogram)

10

Enzyme Characterization

• Determination of optimal pH, temperature, and stability parameters

11

Kinetic Analysis

• Determination of Km and Vmax values • Graphical analysis (Michaelis-Menten plots, Lineweaver–Burk)

12

Evaluation, Discussion, and Workshop Closure

• Group discussion: analysis of results, sources of error, comparison with literature values • Emphasis on scientific interpretation, not just technical success

Sessions

Title

Focus

1

Opening Session: Workshop Introduction and Safety Instructions

• Presentation of workshop objectives, workflow, and expected skills • Concepts of sustainability, circular bioeconomy, and aquatic waste valorization • Laboratory safety, sample handling, and experimental organization

2

Production of Biopeptides from Fish Protein Residues

• Preparation of protein hydrolysates using protease treatment • Optimization of hydrolysis conditions (enzyme/substrate ratio, time, temperature) • Physicochemical characterization: protein content (Kjeldahl/Bradford), solubility, hydrolysis yield

3

Valorization of Crustacean Waste: Chitin and Chitosan Production

• Extraction of chitin from crustacean shells • Deacetylation process for chitosan production • Preparation of chitosan-based materials (hydrogels/microcapsules) • Production of chito-oligosaccharides using chitinase

4

Functional Evaluation of Bioactive Molecules

• Antioxidant activity assays (DPPH, ABTS) • Antibacterial activity evaluation (inhibition assays/microdilution if available) • Statistical treatment: mean, standard deviation, comparison of results

5

Fishmeal Production and Functional Feed Formulation

• Processing fish residues: drying, grinding, and quality assessment • Formulation of functional fish feed supplemented with biopeptides and chito-oligosaccharides • Evaluation of nutritional improvement potential and feed functionality

6

Collagen Isolation from Fish By-products

• Extraction of collagen from fish residues • Determination of extraction yield • Physicochemical characterization: solubility, gel properties, and stability

7

Characterization and Quality Evaluation of Valorized Products

• Comparative characterization of proteins, chitosan derivatives, and collagen • FTIR analysis (if available) • Identification of functional groups and structural properties • Comparison between products and evaluation of performance

8

Economic Analysis and Valorization Potential

• Estimation of material balance and process yield • Preliminary cost analysis at laboratory scale • SWOT analysis of valorization strategies • Discussion of industrial applications and market opportunities

Session

Title

Key Focus

1

Introduction: Why Cross Disciplines?

Icebreakers. Mini-lecture: What is interdisciplinary thinking? Activity: How science, technology, art, and society approach the same problem differently. Assignment: Curiosity Journal - Pick a real-world issue to follow throughout the course.

2

Nature and Engineering: Lessons from Biomimicry

Case studies: Biomimicry in architecture, materials, and technology. Guest talk: Engineer, biologist, or architect. Group activity: Analyze a natural phenomenon and propose an application.

3

Science in Art and Art in Science

Examples: Visual arts inspired by scientific discoveries, and vice versa. Workshop: Analyze artworks and inventions influenced by scientific thinking. Group discussion: How imagination bridges science and art.

4

Social Innovation and Technology

Case studies: How technology has transformed society (positive and negative). Debate: Does technology always improve life? Workshop: Map technological impacts on Algerian society (education, health, economy).

5

Ethics, Innovation, and Responsibility

Exploration: Emerging technologies (AI, genetic engineering, green technologies). Debate: Ethical dilemmas in modern science and technology. Group Challenge: Draft a "Code of Ethics" for future innovators.

6

Interdisciplinary Thinking Day (Student Organized)

Student-Led Event: Students organize a mini-conference or poster session on interdisciplinary thinking. Final Presentations: Each student or group presents a project analyzing a real-world issue through multiple disciplines Group Reflection: Students lead a discussion: How do disciplines connect? What challenges did they face? Closing Activity: Collective creation of a "Commitment Wall" or Manifesto for lifelong exploration and interdisciplinary learning.

Chapter

Title

Main Topics

1

Introduction to the Biobased Economy

- Why develop a biosourced economy? - Biotechnologies supporting the bioeconomy. - Biomass as a renewable resource. - Environmental, economic, and societal benefits of biosourced production.

2

Types of Biobased Products

- Biobased chemicals. - Biobased materials. - Biobased energy. - Emerging sectors and innovations.

3

Applications of Biobased Products

Medical Applications: - Porous scaffolds for tissue engineering. - Drug delivery systems. - Wound healing materials. Microbiological Applications: - Microorganism encapsulation (food industry, probiotics). - Antimicrobial food packaging. Materials and Industrial Applications: - Construction materials and composites. - Paper and packaging industries. - Compost and biobased fertilizers. - Biobased paints, coatings, lubricants, and functional fluids. - Bioplastics:   • Current production landscape.   • Biodegradability and recyclability.   • Applications in biobased packaging.

4

Challenges and Limitations of Biobased Products

- Cost and scalability issues. - Competition with food production. - Regulatory and certification challenges. - Technological barriers.

5

Future Perspectives and Innovations

- Next-generation biorefineries. - Synthetic biology and engineered biosystems. - Circular economy models. - Trends in biobased product development and global markets.

Chapter

Topic

Subtopics

1

Introduction to Programming

- What is a program? Programming languages - Why choose Python for biology? - Examples of applications in science

2

Installation and Getting Started

- Installing Anaconda - Writing your first Python script - Executing cells, saving files, using comments

3

Variables and Data Types

- Primitive types: int, float, str, bool - Tuples, sets, lists, dictionaries - Mathematical and logical operators - Expressions & basic statements (reading, writing, assignment)

4

Control Structures

- Conditional statements: if, elif, else - Comparison operators

5

Loops

- for and while loops - break and continue statements - Iterating through lists

6

Functions

- Defining a function with def - Parameters and return values

7

File Handling

- Reading and writing .txt and .csv files - Methods: open(), read(), write()

Week

Focus

Activities

Deliverable

1

Orientation Session

Introduction to course expectations, overview of bioprocess/biotech sectors, industry etiquette.

Visit Preparation Assignment

2

Visit 1: Biopharmaceutical Manufacturing

Tour of a biopharma plant: fermentation, purification, cleanrooms, GMP compliance.

Field Notes + Site Reflection

3

Seminar: Process Scale-Up Challenges

Guest lecture from process engineers about moving from lab to pilot to full scale.

Short Reflection Essay

4

Visit 2: Agro-Industrial Bioprocess Facility

Visit focusing on microbial fermentation, valorization, and bioeconomy.

Field Notes + Site Reflection

5

Visit 3: Environmental Biotech & Waste Valorization

Visit to a biowaste valorization or bioremediation site. Focus on sustainability and circular economy.

Field Notes + Sustainability Analysis

6

Seminar: Quality and Regulatory Affairs

Guest session with a QA/QC or regulatory specialist (GMP, ISO standards, HACCP, etc.).

Quality System Mapping Assignment

7

Visit 4: Food Biotechnology / Industrial Biotech

Visit focusing on food ingredients, bio-based materials, or bioproducts innovation.

Field Notes + Innovation Report

8

Career Roundtable: Working in Biotech Industries

Panel with engineers, scientists, and managers from visited companies.

Career Skills Reflection

9–10

Team Project Preparation

Students form teams to synthesize what they learned into thematic reports.

Draft Industrial Insights Report

11

Project Finalization

Report finalization and peer feedback.

Final Industrial Insights Report

12

Final Presentations

Team presentations summarizing sector insights, reflections, and recommendations.

Oral Presentation + Peer Feedback

Chapter

Title

Key Topics

1

Introduction to Enzyme Engineering

- Limitations of natural enzymes - Overview of enzyme engineering approaches - Milestones in the development of engineered enzymes

2

Rational Design

- Principles of rational design and structure-based modifications - Selection of target residues - Stability engineering (salt bridges, disulfide bonds, surface charges) - Case studies

3

Site-Directed Mutagenesis

- Molecular techniques for introducing mutations - Primer design and PCR-based mutagenesis - Analysis and verification of mutants - Expression and purification of variants

4

Directed Evolution

- Concepts of natural selection and iterative mutation - Random mutagenesis (error-prone PCR, mutator strains) - Recombination (DNA shuffling, StEP) - High-throughput screening and selection strategies

5

Semi-Rational and Smart Libraries

- Combinatorial active site saturation testing (CASTing) - Iterative saturation mutagenesis (ISM) - Use of bioinformatics to reduce library size - Smart design of combinatorial libraries

6

Computational Tools in Enzyme Engineering

- Homology modeling and structure prediction - Molecular docking and molecular dynamics - Tools: PyMOL, Rosetta, FoldX, AlphaFold

7

Enhancing Enzyme Properties

- Thermostability and pH tolerance - Substrate specificity and enantioselectivity - Solvent resistance and expression yield - Fusion tags and immobilization-ready variants

8

Case Studies and Applications

- Engineered enzymes in biocatalysis, pharmaceuticals, diagnostics, food - Enzyme design for green chemistry - Patents and commercialization examples

Session

Title

Key Activities

1

Designing Primers for Site-Directed Mutagenesis

- Plan mutagenic primers. - Practice designing primers targeting specific amino acid changes.

2

Analyzing Protein Structures to Identify Mutagenesis Targets

- Use structural data (e.g., PDB files) to select key residues. - Visualize active sites, flexible regions, or stabilizing mutations.

3

Designing an Error-Prone PCR Experiment

- Set up an error-prone PCR strategy. - Adjust conditions (e.g., Mn²⁺, dNTP imbalance) for desired mutation rates.

4

Planning and Evaluating a Directed Evolution Screening Workflow

- Design a basic screening or selection plan. - Define screening criteria (activity, stability, specificity) and throughput strategies.

5

Using FoldX or AlphaFold to Predict Effects of Mutations

- Predict effects of point mutations on protein stability. - Visualize predicted structural changes. A predicted structure alone does not establish a change in protein stability.

6

Sequence Alignment and Conservation Analysis for Active Site Mapping

- Perform multiple sequence alignments. - Identify conserved and variable residues for rational mutagenesis.

7

Exploring Successful Enzyme Engineering Case Studies

- Analyze real examples from literature. - Discuss strategies used, outcomes, and lessons learned.

8

Comparative Analysis of Wild-Type vs. Mutant Enzyme Kinetics (Problem Sets)

- Interpret kinetic data (Km, Vmax, specificity constants). - Compare wild-type vs. engineered mutants to evaluate success.

Chapter

Title

Key Topics

I

History of Genetic Engineering

- Key historical milestones in genetic manipulation.

II

Enzymatic Tools for Genetic Engineering

- Restriction enzymes: mechanism, recognition sites, types, nomenclature, methylation, applications. - Other key enzymes: polymerases, ligases, phosphatases, nucleases.

III

Molecular Hybridization Techniques

- Principle of hybridization, Tm, influencing factors. - Liquid-phase and solid-phase hybridization. - In situ hybridization (ISH). - Design and labeling of probes (radioactive and non-radioactive methods).

IV

Vectors for Genetic Engineering

- Concept and properties of vectors. - Plasmids: generations, preparation, replication origin. - Phages: types and use in molecular biology. - Other vectors: cosmids, YACs, BACs, shuttle vectors, viral vectors.

V

Cloning and Expression of Recombinant Proteins

- Principles of cloning (PCR-based cloning, primer and enzyme design). - Construction of genomic and cDNA libraries. - Expression systems (E. coli, post-translational modifications). - Design of expression cassettes. - Overview of heterologous protein production.

VI

Genetically Modified Organisms (GMOs)

- Plant and animal transgenesis methods. - Gene transfer techniques (direct and indirect). - Construction of transgenes. - Applications of GMOs. - Traceability and labeling of GMOs.

VII

New Genetic Engineering Techniques

- Genome editing principles. - Programmable nucleases: zinc finger nucleases, TALENs, CRISPR/Cas9. - RNA interference (RNAi) and emerging methods.

Session

Title

Key Activities

1

Restriction Site Identification and Vector Map Analysis

- Analyze plasmid/vector maps. - Identify restriction sites and plan cloning strategies.

2

Primer Design for Cloning and PCR

- Design forward and reverse primers. - Choose restriction sites. - Check primer parameters (Tm, GC content).

3

In Silico Cloning using SnapGene or Benchling

- Simulate cloning steps. - Visualize insertions, restriction analysis. - Prepare in silico cloning files.

4

Planning Recombinant Protein Expression Experiments

- Select appropriate vectors, tags, and expression systems. - Plan induction, purification steps. - Consider host properties (e.g., E. coli, yeast).

5

CRISPR gRNA Design and Off-Target Analysis

- Design gRNAs using Benchling or CHOPCHOP. - Perform simple off-target prediction. - Discuss criteria for gRNA quality.

6

Case Study Analysis: Biotech Success Stories (Bt Crops, Insulin, GMO Salmon)

- Study genetic engineering projects. - Identify methods used and societal impact.

7

Critical Reading and Presentation of Recent Genetic Engineering Papers

- Select a recent research paper. - Summarize and present objectives, methods, results. - Develop scientific communication skills.

8

Simulation of Southern Blot and Probe Design

- Plan and simulate a Southern blot. - Design hybridization probes. - Discuss hybridization specificity and labeling.

9

Mock GMO Approval Process

- Simulate the regulatory evaluation of a GMO (e.g., EU or USDA frameworks). - Identify biosafety, traceability, and labeling aspects.

10

Ethical Issues in Genetic Engineering (NEW Tutorial)

- Analyze real or hypothetical case studies involving ethical dilemmas (e.g., gene editing in humans, GMO labeling, biodiversity risks). - Group discussion and ethical decision-making.

11

Final Team Project: Proposal for a Genetic Engineering Application

- Teams propose a genetic engineering project (GMO, therapeutic, industrial). - Prepare a poster. - Oral defense of the project in front of peers.

Chapter

Title

Key Focus

1

Importance of Enzymes in Industrial Biotechnology

- Principles and advantages of using enzymes in industrial manufacturing. - Specificity, mild conditions, environmental benefits. - Comparison with traditional chemical processes.

2

Pharmaceutical Applications

- Enzymatic production of pharmaceutical compounds: • Antibiotics: 6-APA production, cephalosporin modification, gramicidine synthesis. • Steroids: hydroxylation, dehydrogenation, side-chain cleavage. - Industrial examples and process optimization.

3

Applications in Fine Chemicals

- Enzymatic pathways for producing amino acids and organic acids: • L-lysine, L-tryptophane, L-DOPA, L-phenylalanine, L-citrulline. • Gluconic acid, malic acid, tartaric acid. - Enzymatic synthesis of specialty chemicals (e.g., acrylamide, nucleotide derivatives).

4

Industrial Applications in Food and Beverage

- Enzymatic production in food industries: • Sweeteners: glucose isomerase for high-fructose syrup. • Saccharose hydrolysis: invertase activity. • Cyclodextrin production. • L-sorbose production for vitamin C synthesis. - Enzyme uses for improving food processing efficiency.

5

Enzymes in Textile Industry

- Applications of enzymes in textile processing: • Biopolishing of fabrics (cellulases). • Denim finishing (stonewashing with cellulases). • Enzymatic desizing to remove starch. - Environmental advantages and industrial challenges.

6

Enzymes in Detergent Industry

- Role of enzymes in detergents: • Proteases, amylases, lipases, cellulases in laundry and dishwashing detergents. • Requirements for enzyme stability (pH, temperature). - Formulation challenges and innovation trends.

7

Enzymes in Cosmetics Industry

- Emerging uses of enzymes in cosmetic products: • Enzymatic exfoliation (e.g., papain, bromelain). • Enzymatic synthesis of bioactive compounds. • Stability and delivery challenges for cosmetic applications. - Trends in biotech-based cosmetic innovation.

No.

Case Study Title

Short Description

1

Science and Risk-Based Approach to Biocatalysis in Pharmaceutical Manufacturing

Presents strategies for safely and effectively integrating enzymes into the manufacture of pharmaceutical APIs, using a science-based and risk-assessment framework to ensure patient safety and product quality.

2

Life Cycle Assessment of Enzymes for Pharmaceutical Applications

Evaluates the environmental impacts (cradle-to-gate) of enzyme production for pharmaceutical uses, analyzing energy, raw materials, waste treatment, and proposing modular estimation techniques for enzyme LCIs.

3

Production of 7-Amino-Cephalosporanic Acid (7-ACA) (Biochemie, Germany/Austria)

Describes enzymatic and fermentation strategies used in the large-scale production of 7-ACA, a key intermediate for cephalosporin antibiotics, highlighting technical innovations and production challenges.

4

Biotechnological Production of Cephalexin (DSM, Netherlands)

Details the industrial enzymatic process for producing semi-synthetic cephalexin, improving antibiotic properties compared to natural cephalosporins, with large-scale fermentation and biocatalysis integration.

5

Manufacture of Riboflavin (Vitamin B2) (Hoffmann-La Roche, Germany)

Chronicles the microbial biotechnological production of riboflavin as a food and feed supplement, showing the industrial scaling of enzymatic and fermentation processes for vitamins.

6

Bioprocesses for Amino Acid Manufacture (Tanabe, Japan)

Explains the development and industrialization of amino acid production processes using immobilized enzymes and microorganisms, comparing innovations across generations of bioprocesses.

7

Manufacture of S-Chloropropionic Acid (Avecia, United Kingdom)

Illustrates the enzymatic production of a chiral intermediate (S-CPA) important for agrochemicals and pharmaceuticals, emphasizing the importance of enantiomeric purity and cost reduction.

8

Enzymatic Production of Acrylamide (Mitsubishi Rayon, Japan)

Describes the industrial enzymatic synthesis of acrylamide, a key chemical used in polymer industries, focusing on production efficiency, green chemistry, and industrial demand.

9

Formulated Product and Process Design in the Detergent Industry

Presents a mathematical optimization-based methodology for simultaneous design of detergent formulations and manufacturing processes, balancing environmental impact, cost, and customer acceptance.

10

Design and Economic Evaluation of Enzymatic Membrane Reactors for Antibiotic Degradation

Investigates the design, cost estimation, and optimization of ceramic membrane reactors using immobilized enzymes for antibiotic removal, focusing on reactor lifetime, enzyme kinetics, and economic viability.

Chapter

Title

Topics Covered

1

Introduction to Downstream Processing

- Overview of bioprocessing: upstream vs. downstream. - Product characteristics and purity requirements. - Classification of DSP operations (cell removal, capture, purification, polishing).

2

Cell Disruption and Solid-Liquid Separation

- Mechanical and non-mechanical cell disruption methods. - Filtration and microfiltration. - Centrifugation (batch and continuous centrifuges).

3

Extraction and Precipitation Techniques

- Solvent extraction principles. - Aqueous two-phase systems. - Precipitation of proteins/enzymes (e.g., ammonium sulfate method).

4

Adsorption and Chromatographic Separation

- Principles of adsorption (isotherms, batch adsorption). - Ion exchange, affinity, size exclusion, hydrophobic interaction chromatography. - Column design, scaling-up, and breakthrough curve analysis.

5

Membrane Separation Processes

- Ultrafiltration and nanofiltration principles. - Reverse osmosis and dialysis applications. - Membrane fouling, cleaning strategies, and design considerations.

6

Drying and Formulation

- Lyophilization (freeze drying) and spray drying. - spray granulation and fluidized bed drying technologies. - Product stabilization, formulation, encapsulation, and controlled release.

7

Process Integration and Case Studies

- Strategies for integrating unit operations. - Process modeling and basic simulation principles. - Real-world examples: DSP for industrial enzymes, antibiotics, and bioactive peptides.

8

Cost, Sustainability, and Regulatory Aspects

- Mass balances: yield, throughput, and cost efficiency. - Environmental impact and waste management in DSP. - Regulatory compliance: Good Manufacturing Practices (cGMP) for bioproducts.

Tutorial

Topic

Key Activities

1

Design of Centrifugation Step

- Calculate required centrifuge size for microbial cell harvest. - Analyze sedimentation principles and performance parameters (g-force, flow rate).

2

Protein Purification Flowchart Development

- Design a full DSP flowchart based on product characteristics (e.g., molecular weight, stability, charge). - Select unit operations: separation, capture, purification, polishing.

3

Yield and Purification Factor Estimation

- Perform mass balance calculations across successive DSP steps. - Compute yield, purification fold, and recovery rate. - Identify bottlenecks in the purification chain.

4

Chromatography Column Sizing and Breakthrough Analysis

- Calculate appropriate column volume based on product load. - Interpret breakthrough curves for resin selection and column optimization. - Understand loading, washing, elution profiles.

5

Comparison of Drying Technologies for Enzyme Products

- Compare lyophilization, spray drying, and fluidized bed drying for a sensitive enzyme product. - Evaluate drying method impact on activity, yield, and cost. - Propose stabilization strategies after drying.

6

Mini-project: DSP Process Design Challenge

- Students work in groups. - Scenario: Given a bioproduct (enzyme, protein, bioactive peptide) and production constraints (purity > 95%, yield > 60%, cost-effective), design a complete downstream process. - Deliverable: Flowchart + mass balance + technology justification + short oral presentation (10 min) or poster. - Focus: Integration of unit operations, optimization trade-offs, basic cost thinking, and regulatory hints (GMP if applicable).

Week

Session Title

Activities / Focus

Outputs

1

Introduction & Project Planning

- Overview of cloning strategies and vectors. - Primer design, vector and host planning.

Project plan: cloning map, primers designed.

2

Preparation of Solutions & Competent Cells

- Media and buffer preparation. - Preparation of chemically competent E. coli DH5α. - Safety & aseptic techniques.

Ready competent cells and sterile media.

3

Genomic DNA Extraction and PCR Amplification

- Genomic DNA extraction. - PCR amplification of the target gene. - PCR troubleshooting.

Verified PCR amplicon (gel electrophoresis).

4

Gel Extraction and Restriction Digest

- Gel purification of PCR product. - Restriction digestion of insert and vector. - Ligation planning.

Purified DNA ready for ligation.

5

Ligation and Transformation

- Set up ligation reaction. - Transformation into E. coli DH5α. - Plating and incubation.

Transformed colonies grown.

6

Screening of Recombinants

- Colony PCR screening. - Plasmid extraction (mini-prep). - Verification by digestion and gel.

Confirmed recombinant plasmid.

7

Subcloning into Expression Host

- Transformation into E. coli BL21(DE3). - Induction test (small scale). - SDS-PAGE check.

Preliminary expression data.

8

Expression Optimization

- Test different IPTG concentrations, temperatures, induction times. - Quantify expression (SDS-PAGE, densitometry if possible).

Optimized expression conditions.

9

Protein Purification (Affinity Chromatography)

- Cell lysis. - Affinity purification (e.g., His-tag). - SDS-PAGE analysis of fractions.

Purified protein sample.

10

Enzyme Activity Assay

- Perform enzymatic or fluorescence activity tests. - Calculate specific activity, yield.

Activity data and analysis.

11

Troubleshooting & Final Characterization

- Troubleshoot critical steps if needed. - Discuss purification efficiency, expression levels, and limitations.

Finalized experimental data.

12

Project Presentation & Evaluation

- Oral or poster presentation. - Group discussion and feedback. - Submission of final written report.

Final report and defense.

Week

Title

Activities / Focus

1

Introduction to Process Simulation Tools

- Install and set up COCO Simulator or DWSIM. - Interface overview: flowsheets, unit operation library. - Basic data input: components, phases, units.

2

Material Inputs and Property Setup

- Define raw materials and streams. - Set up physical properties (e.g., density, viscosity, solubility for water, glucose, biomass). - Enter mass flow rates, concentrations.

3

Modeling Bioreactors

- Model a batch fermenter using a generic reactor module. - Define reaction stoichiometry (e.g., glucose → biomass + product). - Set yields, conversion, residence time.

4

Downstream Processing I: Filtration and Centrifugation

- Model solid-liquid separation (basic filtration and decanter centrifuge). - Set up cell harvest after fermentation.

5

Downstream Processing II: Extraction and Drying

- Model solvent extraction (liquid-liquid separator). - Simulate basic drying (air dryer unit as proxy for spray drying).

6

Energy Balances and Heat Exchangers

- Add heating/cooling units to fermenters and dryers. - Track utility consumption (steam, cooling water).

7

Scheduling Batch Processes

- Simulate batch operations using simplified scheduling (block diagram logic). - Discuss batch cycle times and bottlenecks.

8

Sensitivity Analysis

- Vary reaction conversion and separation efficiency. - Analyze the impact on yield, throughput, and energy consumption.

9

Case Study Preparation I: Process Setup

- Students choose a case (e.g., Lactic Acid Fermentation, Enzyme Production). - Define material inputs, basic reactions, and process units needed.

10

Case Study Preparation II: Simulation and Troubleshooting

- Build complete flowsheets. - Run simulations, fix convergence issues, validate material and energy balances.

11

Report Generation

- Extract simulation outputs: material balances, energy balances, utility use. - Prepare flow diagrams and techno-economic estimates.

12

Project Presentation and Feedback

- Students present flowcharts and basic economic analysis. - Peer feedback + instructor feedback. - Final submission of simulation report.

Unit

Title

Detailed Topics

1

The Entrepreneurial University and University 4.0

Evolution of universities from 1.0 to 4.0 Characteristics of University 4.0 Digital transformation and artificial intelligence in higher education The role of universities in the knowledge economy Valorisation of scientific research Transformation of research outputs into startups Universities as drivers of innovation and economic development International examples of entrepreneurial universities such as MIT, Stanford, Cambridge, Tsinghua, NUS, TUM and PSL/Polytechnique.

2

Entrepreneurship and Innovation Ecosystem in Algeria and the University

Definition of the entrepreneurial ecosystem Key actors in the ecosystem Algerian policy for innovation support Incubators and accelerators; Investment funds Ministerial Decision 1275 (Startups ; Micro-enterprises ; Patents) University incubators and technology-support centres Role of artificial intelligence in the ecosystem Linking universities with the economic environment.

3

Introduction to Startups and Lean Startup Methodology

Difference between traditional companies and startups Concept of innovation Uncertainty in entrepreneurial projects Origins of the lean startup approach Core principles of the methodology Validated learning Reducing waste Build–Measure–Learn cycle Innovation accounting Difference between traditional accounting and innovation accounting Measuring progress under uncertainty. Learning Metrics instead of Profit Metrics

4

Market Understanding and Customer Discovery

Stages of startup creation: idea, team, prototype, investment Steve Blank’s methodology Customer Development: understanding the market and customer behaviour Problem identification Analysis of customer needs Entrepreneurial interviews Building hypotheses Problem–Solution Fit

5

Business Model Canvas

Concept of the Business Model Canvas Value proposition Customer segments Channels Revenue streams Financial structure / Cost structure

6

Minimum Viable Product — MVP

Concept of the MVP Types of MVP: digital/experimental/service/ fake-door Hypothesis testing Rapid prototyping Prototype development tools Digital and industrial MVPs How to measure failure in the shortest possible time

7

Artificial Intelligence and TRIZ for Innovation

Artificial intelligence in entrepreneurship Idea generation Market analysis MVP development Smart marketing TRIZ methodology Technical contradictions Ideal Final Result Combining AI with TRIZ Deep Tech Startups

8

Measurement, Analytics and Failure Management

KPIs — Key Performance Indicators Startup management Leading innovation teams Concepts of growth measurement in startups AARRR Metrics: a method for measuring startup development through five stages: Acquisition: How do we reach and attract customers? Activation: Does the user try the product for the first time? Retention: Do users come back to use it again? Revenue: Does the project generate income/profit? Referral: Do users recommend the product to others?

9

Pivot or Persevere

Concept of Pivot: partial or complete strategic change Concept of Persevere: continuing with the current direction When to change direction? Types of Pivot Decision indicators

10

Funding, Growth and Scaling

Initial funding Self-financing / bootstrapping Investors Angel investors Venture capital Crowdfunding Funding stages Growth Hacking Engines of Growth

Session

Title

Focus

1

Case Study: MIT and the Entrepreneurial University

Analyse why MIT succeeded in creating thousands of startups; identify the relationship between research and innovation; explain the role of incubators and accelerators; compare MIT with Algerian universities; propose a plan to transform an Algerian university into a University 4.0.

1

Workshop: Designing an Algerian University 4.0

Work in teams to design an innovation centre, business incubator, business accelerator, technological support and innovation centre, subsidiary company and university investment fund; submit an integrated organisational roadmap for a University 4.0 model.

2

Case Study: Journey of an Algerian Startup

Select an Algerian startup that obtained a startup label; analyse the actors that supported it; identify its funding sources; map its ecosystem; propose mechanisms to accelerate its growth.

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Workshop: Mapping the Entrepreneurial Ecosystem

Use Miro or Canvas to map the actors of the Algerian entrepreneurial ecosystem: universities, research centres, incubators, accelerators, investors, banks, companies, public agencies, startups and innovators; show relationships between actors and present improvement proposals.

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Case Study: Failure of a Technology Startup

Analyse a startup that spent resources before validating market need; identify the mistakes and sources of waste; propose how Lean Startup could have reduced risk; design an alternative Build–Measure–Learn cycle.

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Workshop: Dropbox and Lean Validation

Analyse how Dropbox validated demand before developing the full product; identify the tested assumptions; compare the cost of the experiment with the cost of full product development; explain the value of early validation.

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Case Study: An Artificial Intelligence Platform for Students

Students analyse a proposed AI-based academic assistance platform. They formulate 10 hypotheses, prepare an interview guide, conduct 20 field interviews, and extract the real problems faced by students. The expected output is a validated problem statement supported by interview evidence.

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Workshop: Entrepreneurial Interviews

Students simulate entrepreneurial interviews by playing the roles of entrepreneur, potential customer and investor. They practise asking questions, collecting feedback and analysing interview results. The expected output is a short report showing validated assumptions, rejected assumptions and key customer insights.

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Business Model Canvas Workshop

Build a complete Business Model Canvas for a selected project; define the value proposition, customers, channels, revenue streams, partners and costs; defend the model before the class or an evaluation committee.

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Case Study: A Smart Delivery Application

Students analyse a smart delivery app project with a limited team budget. They design the lowest-cost MVP, identify the critical hypotheses to test, choose the most appropriate MVP type, and define clear success and failure indicators. The expected output is an MVP design plan with testable assumptions and evaluation criteria.

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Workshop: Building a Real MVP

Students build an initial MVP or prototype using tools such as Figma, Glide, Bubble or Canva. The prototype may be developed during the session or completed at home. The expected output is a simple functional or visual prototype that can be used for customer testing.

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Case Study: A Smart Agriculture Startup

Students analyse a smart agriculture startup aiming to increase production while reducing water consumption. They identify the technical contradiction, apply TRIZ principles, use generative AI assistants to generate solutions, and evaluate the proposed solutions. The expected output is a set of justified innovation solutions based on AI-assisted ideation and TRIZ reasoning.

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Workshop: AI Innovation Sprint

A 90-minute sprint, students use only AI tools to generate an innovative idea, define an MVP and build a preliminary business model. The expected output is a short innovation concept including the problem, proposed solution, MVP and business model structure.

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Case Study: An E-learning Platform

Students analyse an e-learning platform using basic startup data: 10,000 visits, 1,000 registrations, 400 active users and 40 paid customers. They calculate AARRR indicators, identify the main bottleneck, suggest improvement actions, and decide whether the project is progressing toward Product–Market Fit. The expected output is a short analytical report based on startup metrics.

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Workshop: Startup Dashboard

Students build a startup dashboard including Acquisition, Activation, Retention, Revenue, Referral and Burn Rate. They interpret the results and explain how the dashboard can guide startup decisions. The expected output is a simple visual dashboard with comments on performance, weaknesses and recommended actions.

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Case Study: Instagram — From Burbn to Instagram

Students analyse the transition from Burbn to Instagram as an example of Pivot. They identify the reason for the Pivot, the data that supported the decision, the results achieved, and possible alternative strategic choices. The expected output is a short case analysis explaining why the Pivot was justified.

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Workshop: Board Meeting Simulation

Students analyse a startup file including performance indicators, customer feedback and financial data. They simulate a board meeting and take a collective decision: Pivot, Persevere or Kill Project. The expected output is a justified strategic decision supported by statistics, evidence and numbers.

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Semester-long Startup Lab Project

Students develop a startup project throughout the semester. The project includes selecting a real problem, conducting Customer Discovery, preparing a Business Model Canvas, designing an MVP, using AI and TRIZ tools, measuring and analysing results, making a Pivot/Persevere decision, preparing a funding and growth plan, and presenting a final pitch. The expected output is a complete startup project file and final pitch presentation.