• Course title: ISB103: Academic Induction
• Number of ECTS: 2
• Course code: MMCB-2
• Module(s): Module 1.1
• Language: EN
• Mandatory: Yes

This introductory week consists of 3 parts:(i) Learning about the structure and rules of your Master study line.(ii) Familiarization with protein primary (amino acid sequence) and tertiary structure. Getting to know commonly used methods to study proteins.(iii) A brief overview of ethics in academic writing (e.g. plagiarism), how to properly handle references, and how to structure a typical scientific report.

Understanding the structure and rules of your study lineRe-familiarize yourself with protein structuresBeing able to write reports for the upcoming experimental and computational courses

Overview lecture and Q/A session to study line structure and rulesLecture and exercises to use the free protein structure visualization software Chimera.Seminar with short presentations about common protein methods.Lectures on ethics and academic writingCPE 1 title: Introduction to protein structureDescription: Learning and familiarization with proteinogenic amino acid structure. Application of the software Chimera to visualize 3D protein structure. Recognition of amino acid side chains within a protein structure.Course instructors: Daniel Abankwa, Carla DuvalCPE 2 title: Introduction to protein methodsDescription: Student seminar short presentations describing assigned methods to study proteins. Course instructors: Daniel Abankwa, Sara BottoneCPE 3 title: Introduction to academic writingDescription: This class provides a brief overview of ethics in academic writing (e.g. plagiarism), how to properly handle references, and how to structure a typical scientific report, e.g. introduction, materials and methods, and results.  Course instructors: Evan Williams 

Assessment modalityContinuous assessmentAssessment tasksType of assessmentGrading schemeWeight for final gradeTask 1Written exam20 points (0-20)Full exam 40%ObjectivesRecognize amino acids within a 3D protein structureAssessment rulesCorrect responseAssessment criteriaCounts of correct responsesTask 2Presentation20 points (0-20)10%ObjectivesPresent in 5 min an assigned method to study proteins.Assessment rulesPresentation quality judged by peers and instructorAssessment criteriaCumulative ScoringTask 3Written exam20 points (0-20)50%ObjectivesProper citations, plagiarism identification, recognize proper scientific writing styles (e.g. objective, impersonal)Assessment rules4 quizzes in MoodleAssessment criteriaCounts of correct responses

• Course title: ISB811: Biosafety and Introduction to Cell and Molecular Biology
• Number of ECTS: 3
• Course code: MMCB-1
• Module(s): Module 1.1
• Language: EN
• Mandatory: Yes

Getting an overview on working in a bioscience laboratoryAbility to design and perform experiments in modern bioscienceUnderstanding of the safety regulations in a bioscience laboratory

Safety regulations in bioscienceSterile workingOrdering reagentsPreparing solutionsDesigning and organizing experimentsAnalysis of dataPresentation of research results

Learning material   Instruction hand-outs, PDF-files of method articlesTeaching methods and assessmentObligatory attendance, summary protocol

• Course title: ISB101: Genomics / Databases
• Number of ECTS: 5
• Course code: MMCB-3
• Module(s): Module 1.1
• Language: EN
• Mandatory: Yes

This course introduces the theory and practice of current concepts in genomics and genetics, particularly to introduce the genome as the basic foundation for systems biology. Topics include overview of genomes, sequencing and mapping, comparative genomics, population genetics and genomics, basic bioinformatics, population-level and rare variation analysis (SNPs, indels), functional genomics and clinical genomics. The course familiarizes students with the tools and principles of genomics, with a focus on the requirement for efficiently processing high volumes of data. By the end of the course, students will have a working knowledge of current genomics technologies and approaches as well as the types of databases and computational tools available.

Learn the fundamentals molecular biology and biochemistry background for genetics and genomics.Obtain an overview on how current sequencing technologies work and how to analyse the data.Introduce programmatic data analysis in R.Become familiar with common, large biological databases routinely used in genomics and genetics, and how to retrieve and analyse these datasets.Learn scripting the R programming language as well as searches with regular expressions.Develop familiarity with command line interface of Unix shells for data transfer and handling.After the course, students will understand how to perform large-scale data analyses on networked computers for genomics and related disciplines.

The course consists of half-day lecture segments on genetics and genomics technologies and five half-day lecture segments data analysis in R in the first week. The second week introduces a project to be conducted in groups that revisits key elements of the lectures in practical.

Total grade is composed of graded exercises in R, (30%), a graded report (35%) and written exam on genomics (35%).

Key words: databases, genomics, next-generation sequencing (NGS), single-nucleotide polymorphism (SNP), genome-wide association studies (GWAS), R, data analysis

• Course title: ISB201: Gene Regulation / Transcriptomics
• Number of ECTS: 5
• Course code: MMCB-4
• Module(s): Module 1.2
• Language: EN
• Mandatory: Yes

Week 1: After DNA replication, certain parts of the genome are transcribed into mRNA. This process is extremely well regulated and coordinated to allow for cell- and situation-dependent expression of necessary gene products. MISB201 is teaching a solid understanding of how gene expression works in mammalian cells and how it is regulated at all known levels. Week 2: An introduction into the most common language R to analyse high throughput gene expression data coming from various RNA Seq or single cell Seq. Explanations and hands-on exercises to learn to use: Data retrieval, Database use, Data formatting, Statistics QC of RNA Seq data, RNA Seq data analysis, and Sc Seq data analysis.

Overview of transcriptomics (first week)

Learn critical thinking and approaching complex contents in a relatively short period of time, enhance self-study skills to repeat and recap the taught material. Interactive group exercises in class are included to enhance interactions and understanding.

Have a solid understanding of how gene expression works in a mammalian cells, how it is regulated at the various cellular levels, which types of RNA are generated and what functions they have in the cell, how gene expression can be measured and manipulated and how the data retrieved from high throughput technologies are handled and analysed.

1.  The topic and putting gene transcription into a general context of cellular life cycles;2.  Epigenetic mechanisms involved in gene expression; 3. Transcription machinery assembly at the promoter and the transcriptional process itself;4.  Post-transcriptional regulatory mechanisms (fine-tuning the amount of expressed genes);5.  Types of transcribed RNAs with a focus on lnc and miRNAs;6.  Technologies to measure and quantify gene expression.7.   R to analyse high throughput gene expression data coming from various RNA Seq or single cell Seq8.   Data retrieval, Database use, Data formatting, Statistics QC of RNA Seq data, applications of up-to-date bioinformatics tools and packages (as these are changing, this will be updated regularly) 

Written exam           

• Course title: ISB301: Protein Structure and Function
• Number of ECTS: 5
• Course code: MMCB-5
• Module(s): Module 1.2
• Language: EN
• Mandatory: No

Solid knowledge of how proteins function as ‘molecular machines’

Understand general ‘rules’ and common principles in protein activity regulation

Understand the generic architecture of proteins and protein mediated processes (enzyme catalysis, signalling)

Learn about the evolutionary principles that are exploited to create the diversity of proteins

Apply knowledge to the difficult question of drug discovery

In the main lecture we will use a mix of classical theory- and methods-focused lectures, flipped classroom teaching, Kahoot-formative testing and exercises to provide you with an intensive training in modern protein biology.We will start by reviewing basics of chemistry that apply to protein biochemistry and repeat the fundamentals from amino acids to secondary structures. Next we have a look at the basic building blocks of proteins, domains, and learn how these combine to form new functional entities. Then we look at how proteins react as enzymes and with each other, how they are modified, and which factors determine how fast they react. In the fourth section, we look at how major signalling pathways function on the protein-structural level, before we in the fifth section look at drug discovery. We learn about basics in drug discovery and will apply our knowledge from all the sections in group exercises to formulate steps necessary in drug discovery.These theoretical sections are supported by method focused lectures, where we learn about common tools in protein biochemistry. This includes, the structure and application of antibodies e.g. in Western blotting, bio/physical techniques to study protein-protein interactions in vitro and in cells, basics of protein structure determination and common assays in drug discovery.Additional lectures and exercises will introduce you to the use of protein databases and computational protein structure analysis.In an accompanying seminar you will elaborate a presentation on a protein science topic and present it to the class.Last but not least, you will gather hands on experience in a practical that will introduce you to basic techniques of protein biochemistry, such as Western blotting.

Final written examTwo Quick Tests during the lectureReport and contribution to practical (TP)Seminar presentation

BibliographyHow proteins work (Mike Williamson) Garland Science, ISBN-10: 9780815344469https://www.amazon.com/How-Proteins-Work-Mike-Williamson/dp/0815344465/

• Course title: ISB302: Proteomics
• Number of ECTS: 5
• Course code: MMCB-6
• Module(s): Module 1.2
• Language: EN
• Mandatory: No

Students trained in this course will be able to design a basic cellular experiment that involves proteomic profiling using LC-MS/MS. Students will be able to differentiate various technologies (instrumentation, enrichment strategies, protein identification and quantification) in the field of proteomics, and be able to compare their capabilities and limitations for biomedical research. Home work and quiz will focus on data interpretation using mass spectra acquired from peptides, from which students will be able to identify proteins (both by de novo sequencing and using a database search engine). We introduce reverse-phase protein array (RPPA) as a cross validation technology. Students will understand the principle of protein microarrays and be able to compare the analytical aspects of RPPA and LC-MS in phosphoproteomics.

Biological mass spectrometryMass spectrometry-based proteomicsAnalytical strategies for proteins (enrichment, separation, identification and quantification)PhosphoproteomicsProtein microarray

(1) Biological mass spectrometry and its application- Mass spectrometry- Liquid chromatography- Protein chemistry for MS-based proteomics- Peptide sequencing- Protein identification- Protein quantification- Proteome profiling and sample preparation- PTM studies- Proteomics in biomedical research- Proteomics in clinic- Proteogenomics(2) A case study of phosphoproteomics- Introduction of phosphoproteomics- Phospho-enrichment and biochemical processing (wet-lab)- LC-MS/MS (MS lab) and data analysis(3) Cross-validation of phospho signaling- Introduction of protein arrays- Protein extraction (wet-lab)- RPPA (protein lab) and data analysis

Attendance (10%), Home Work (20%), Quiz (30%), and Report (40%)

Support:Handout: A booklet prepared by lecturers will be provided.

• Course title: ISB202: Practicals in Gene Regulation
• Number of ECTS: 5
• Course code: MMCB-7
• Module(s): Module 1.3
• Language: EN
• Mandatory: No

Practical approach to transcriptomics: experimental manipulation of gene expression

Learning to manipulate gene expression in cancer cells

Analysis of transcriptomic high throughput data and selection of interesting target genes for validation

Perturbation of gene expression of selected target genes

Extraction of RNA from cultured and manipulated cancer cells

Measuring gene expression levels by qPCR

Performing wet lab experiments

Understanding principles of practical gene level perturbation

Analyse and select high throughput data (RNAseq) to identify single targets of interest

Experiencing and performing tissue culture, cancer cell treatment/stimulation, RNA extraction + quantification and qPCR to measure affected gene expression levels: standard measure to quantify gene expression

Understanding principles, data analysis and QC aspects of qPCR

Generating and critically analysing own data

Analysing other, supplied data (Western Blot) in relation with generated data

Designing own qPCR experiment with all relevant controls

Working in a team in a wet lab environment

Writing a detailed scientific report

Practical work in teaching lab, lectures, data analysis:Melanoma tissue cultureTreatment of cells with cancer drugs (targeted therapy)RNA extraction and quantificationReverse TranscriptionqPCR with data analysis of own resultsIntroductory lecture on the course (theory and practical details), lectures on RNA+RNA extraction and qPCR data analysisBioinformatic analysis of RNAseq data generated in Signal Transduction lab

Assessment modality Combined assessment

Assessment tasks Type of assessment Grading scheme Weight for final grade

Task 1 Take-home assignment20 points (0-20)75Objectives Final reportAssessment rules Written reportAssessment criteria Quality of report writing, presentation of scientific results generated in the wet lab course, understanding of the results and interpretation, troubleshooting capacity, correctness of scientific results and provided tasks

Task 2 Written exam Knowledge test during the course20 points (0-20)10Objectives Testing knowledge of provided course material and scripts, standard wet lab calculationsAssessment rules Written testAssessment criteria Performance

Task 3 Active participation Practical lab work20 points (0-20)       10Objectives practically planning and performing molecular biological experiments; generating interpretable scientific data; observing safety rules and punctualityAssessment rules Presence in the lab, active participation, pipetting skills, level of understanding of required tasksAssessment criteria Motivation, performance (wet lab skills)

Task 4 Active participation High throughput data analysis20 points (0-20)5Objectives Bioinformatic analysis of transcriptomic high throughput dataAssessment rules Active participationAssessment criteria Performance, finding the requested target genes           

• Course title: ISB701: Introduction to Systems Biology
• Number of ECTS: 5
• Course code: MMCB-8
• Module(s): Module 1.3
• Language: EN
• Mandatory: No

Getting an overview on the elements of systems biology and its concepts and applications; Ability to analyze biological processes by systems biology methods and concepts; Understanding of the principles of systems biology, such as topology, stochiometry and kinetics

Recall and apply key procedures and methods in mathematics and bioinformatics; Differentiate the key principles of bottom-up systems biology; Integrate basic understanding of bottom-up systems biology by designing, creating and analyzing models

Definition of systems biology; Basic concepts in systems biology; Biophysical basis of enzyme reactions; Math recap: Matrices; Linear Equations and Ordinary Differential Equations; Balancing and Modelling; Model Analysis (Steady States, Stability, Phase Portrait, Bifurcation plot); Network motifs; Application examples

Combined assessment

Written exam

Detailed Course Handbook including links to deepening youtube videos, as a basis for independent studying during this flipped-classroom course.

• Course title: ISB702: Pharmacokinetics
• Number of ECTS: 5
• Course code: MMCB-9
• Module(s): Module 1.3
• Language: EN
• Mandatory: No

Getting an overview on the elements of pharmacology & pharmacokinetics (PK) and its concepts and applications; Ability to model and analyze simple PK processes; Develop, run and present own PK model based on ordinary differential equations

Recall and apply key procedures and methods in modelling and model analysis; Understand and Differentiate the key principles of PK; Integrate basic understanding of PK applying dynamical modelling within the Matlab framework

 Courses content:Introduction to Pharmacology and Pharmacokinetics:Definition of pharmacology and PK; Basic concepts in PK: ADME – Absorption, Distribution, Metabolism, Elimination; PK models and application examples;  Safety pharmacologyPharmacokinetic modelling:Introduction IQMtoolbox within Matlab; Modelling case studies ; Modelling project: Develop, run and present own project idea, with the help of tutors

Continuous assessmentWeek 1Written exam Multiple choiceWeek 2Written exam Multiple choicePresentationPitch and present own project

• Course title: ISB104: Translational biomedical research in neurodegeneration – from bed-to-bench-to-bedside
• Number of ECTS: 5
• Course code: MMCB-10
• Module(s): Module 1.3
• Language: EN
• Mandatory: No

Introduction to clinical and translational medicine 

Introduction into precision medicine 

Practical experience of recruitment of study participants 

Processing of patient’s bio-samples for molecular profiling (RT-QuIC)

Patient-derived cellular disease models

Lab automation  

Use of patient derived cellular disease models for phenotypic drug screening 

Designing of a Clinical Study including arms, events and Case Report Forms (CRFs) 

Introduction to Electronic Data Capturing (EDC) system – REDCap 

Cross-talk between clinician, data scientist and lab scientist

FAIR principles and data FAIRification of data (making data Findable, Accessible, Interoperable and Reusable) 

Clinical data curation, harmonization and basic analysis 

Different types of clinical trials and expected outcomes

Biomarkers for precision medicine 

Translation into care and prevention 

This course focuses on the introduction to translational biomedicine, a rapidly growing discipline across different biomedical research discipline. It aims to (i) identify unmet needs together with people with Parkinson’s disease, (ii) to accelerate the transfer of knowledge generated on the bench (laboratory) to be translated back to bedside (clinical trials and care). This course will introduce the clinical and translational medicine field, addressing its evolution and fundamental concepts including (i) domain expertise, (ii) interdisciplinary collaboration and (iii) outreach and communication, with concrete examples in the context of neurodegenerative diseases e.g. Parkinson’s disease (PD). Students will have the opportunity to visit the Parkinson’s Research Clinic (PRC) at CHL (Centre Hospitalier de Luxembourg) and experience the daily clinical research routine and recruitment of people with PD for clinical studies. This course will also include hands-on laboratory practice of how researchers process the collected bio-samples from people with PD and make them available for subsequent molecular (e.g sequencing) and cellular (e.g. induced pluripotent stem cells) profiling and drug screening. In addition, this course will also introduce into biocomputational expertise, i.e. how to design a case report form (CRF), capture data from a clinical study using an electronic data capturing system (e.g. REDCap), how to curate and FAIRify (making data Findable, Accessible, Interoperable and Reusable) the collected data and finally analyze the curated data for unlocking the potential of deep phenotypes patient cohorts for an earlier diagnosis and a better treatment.  Overall the course integrates biocomputational, biological and medical expertise for a comprehensive translational concept.

First session

Written exam (50%)

Report of laboratory work (50%)

Retake exam

Oral exam

The Fundamental Characteristics of a Translational Scientist DOI: 10.1021/acsptsci.9b00022

Electronic Data Capturing (EDC) system – REDCap short video (5min)

FIAR principles publication

• Course title: Français général A1.1 (Belval)
• Number of ECTS: 3
• Course code: LC_CAT-257
• Module(s): Module 1.6 Language courses (Optional)
• Language: FR
• Mandatory: No

Communicative skills in French:- introduce oneself, get in touch with someone and introduce someone (name, age, nationality, profession, spelling);- talk about one’s daily environment (address, e-mail, telephone number, talk about one’s family, hobbies);- ask and give news about someone;- know how to find your way: directions/give instructions;- know how to ask for information (orally and in writing);- ask for the time;- write a simple, short message or fill in simple registrations forms with your personal details

After completing this course, you will be able to use familiar everyday expressions and basic phrases. You can introduce yourself and ask and answer questions about personal details. You can interact in a simple way, provided that the other person talks slowly and clearly and is prepared to help.

This is a general French course, where written and oral comprehension, vocabulary, grammar and spelling are worked on, as well as written and oral expression in French. This course is designed for students with no prior knowledge of French.From the beginning of this course, you will start communicating in French. The covered topics include: greeting, introducing yourself, talking about yourself and your family, describing a city and a neighbourhood, talking about your hobbies and interests. The necessary grammar is explained and ample attention is paid to vocabulary. All skills are covered: speaking, writing, reading and listening. Attention is also paid to the cultural context of Luxembourg.

Continuous assessmentYour final grade will be divided into:•attendance (compulsory) + participation in class: 20%,•2 tests based on oral and written comprehension: 30% •Final test: 50%

BibliographyBonjour et bienvenue A1.1 – tout en français – Livre-cahier + didierfle.appISBN 978-2278110803100% FLE – Grammaire essentielle du français A1 – livre + didierfle.appISBN978-2278109234

• Course title: Français général A2.1 (Belval)
• Number of ECTS: 3
• Course code: LC_CAT-126
• Module(s): Module 1.6 Language courses (Optional)
• Language: FR
• Mandatory: No

Cours en présentiel – campus Belval

Ce cours a pour but de renforcer vos connaissances et vos pratiques en langue française, principalement écrite, afin d’enrichir vos productions d’écrits, non seulement dans le cadre de vos études ou de votre métier mais aussi dans les situations de communication avec d’autres personnes.

A l’issue de ce cours vous serez capable de :• Demander et donner des informations sur des habitudes quotidiennes, un emploi du temps• Parler de vos goûts, de vos projets• Faire des suggestions et réagir à des propositions (acquiescer, accepter, s’excuser)• Donner une raison ; expliquer vos choix• Demander et donner des conseils• Parler de votre expérience professionnelle, de votre environnement de travail• Raconter des événements passés, un souvenir, une anecdote, une expérience.

Dans une première partie, nous évaluerons vos besoins et ferons quelques révisions de grammaire telles que :Utilisation du présent, du présent progressif, du passé récent et du futur procheL’interrogation : qui, quoi, comment, est-ce que, quand, combien, …Conjugaison des verbes essentiels : faire, pouvoir, devoir, vouloir, savoir, connaître …Expression du temps : dans, depuis, il y aUtilisation des adjectifs possessifsLes lieux importants de la vie quotidiennela descriptionles directionsles professionsPuis nous approfondirons ces acquis et les enrichirons en travaillant principalement sur des documents authentiques issus de la vie quotidienne

L’évaluation se

fera

ainsi

:

 

Deux devoirs à la maison à rendre en semaine 4 et semaine 8 (coefficient 1)

Un devoir en classe lors du dernier cours (coefficient 2)

Les

devoirs

comprendront

des

exercices

de

grammaire, de vocabulaire et la

rédaction

d’un

court

texte

personnel.

La présence aux cours est obligatoire afin de valider les crédits ECTS attribués au cours de français général A2. Au-delà de trois absences, l’étudiant/étudiante ne peut plus valider le cours.

 

BibliographieAlter Ego+, Niveau A1-A2, Editions Hachette Objectif Express 1 et 2, Editions HachetteGrammaire essentielle du français A2, 100% FLE, DidierFle

• Course title: Français académique B1 (Belval)
• Number of ECTS: 3
• Course code: LC_CAT-182
• Module(s): Module 1.6 Language courses (Optional)
• Language: FR
• Mandatory: No

 L’objectif de ce cours est d’acquérir les connaissances suffisantes en français pour accéder au cours de niveau universitaire B2. Cette remise à niveau est faite grâce à : des exercices de compréhension orale, de compréhension écrite. À l’oral seront mis en place des jeux de rôles, des présentations et des débats. Nous élaborerons également des cartes mentales qui faciliteront l’acquisition du vocabulaire. Nous nous attarderons également sur la rédaction de différents genres de texte dont nous détaillerons la structure. Toutes ces activités seront ludiques, répondront à des besoins concrets. Les modalités de travail seront variées : travail en grand groupe, en binômes, individuel afin de favoriser la collaboration entre pairs. Le contenu sera adapté selon les besoins du groupe, ainsi vous pourrez commencer le semestre suivant sur des bases solides.

A l’issue de ce cours vous serez capable de : • lire des articles sur des questions contemporaines• comprendre différents points de vue• comprendre un texte littéraire contemporain• écrire des textes clairs et détaillés sur des sujets relatifs à vos intérêts• écrire un essai ou un rapport sur un sujet précis de manière concise, claire, et efficace• exposer son argumentation• mettre en valeur son opinion sur un événement ou une expérience 

Ce cours a pour but de renforcer vos connaissances et vos pratiques en langue française, notamment à l’oral et à l’écrit afin de répondre aux exigences du cadre universitaire et de votre future carrière. Dans une perspective actionnelle, nous travaillerons sur des documents authentiques tels que des articles de presse ou des extraits vidéo. C’est à travers notre corpus que nous aborderons la grammaire et le vocabulaire, outils au service de vos besoins de communication. Vous déduirez les règles de grammaire à partir d’exemples concrets du corpus et les mettrez en pratique à travers plusieurs exercices ludiques.Le travail de production écrite sera décliné sous plusieurs formes : donner ses arguments sous la forme d’une liste d’idées la rédaction d’une réclamationune lettre officielleun résumé d’articleun article argumenté (2 pages maximum) sur un sujet de votre choix.  

25% : Notes des devoirs écrits rendus50% : Compréhension écrite et rédaction d’un article (maximum 2 pages) après une séance de révision en cours.25% : Participation orale en cours et la préparation des devoirs maison. Un maximum de 2 absences est accepté.

Bibliographie  Édito B1, Éditions Didier, 2018 Grammaire essentielle du français, B1, Didier, 2015 Cosmopolite B1, Hachette, 2018 

• Course title: ISB901: Master Thesis
• Number of ECTS: 30
• Course code: MAISB-29
• Module(s): ISB09: Master thesis
• Language: EN
• Mandatory: Yes

Getting an overview on scientific working in a specific field of bioscienceAbility to perform experiments in an own research projectDetailed understanding of the background in own research project

Studying literature in the fieldPerforming own research projectAnalysis of data and creation of figuresWriting a master thesis

Writing own M.Sc. thesis.