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Cell Biology and Genetics

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CBG

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Academic year 2020/2021

Course ID
SCB0198
Teaching staff
Prof. Isabelle Perroteau (Coordinator)
Prof. Adriano Ceccarelli
Dott.ssa Claudia Giachino
Prof. Saverio Francesco Retta
Year
1st year
Teaching period
First semester
Type
Basic
Credits/Recognition
11
Course disciplinary sector (SSD)
BIO/13 - biologia applicata
MED/03 - genetica medica
Delivery
E-learning
Language
English
Attendance
Mandatory
Type of examination
Written and oral
Prerequisites
B2 English level
IMAT biology program
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Sommario del corso

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Course objectives

CBG is a basic course in modern medical education, the purpose of which is to make medical students master the structure and functions of cellular components, as well as genetic regulation and mechanisms; and know the development and trends of the science and the application of new technology. This knowledge will provide a solid foundation for studying other related courses (basic and clinical). 

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Results of learning outcomes

  • Deep knowledge and understanding of cell structures and the dynamic functional activities of cells, cell communication, proliferation and survival
  • Awareness that all pathologies result ultimately from dysfunctions - of genetic or environmental origin - in cellular activities. 
  • Ability to critically interpret the scientific data present in the relative international literature.
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Course delivery

Instructional techniques include direct instruction, question and answer, problem-solving and discovery learning. Molecular Genetics and part of Cell Biology is delivered using the flipped classroom instructional strategy. Students gain first exposure to new material outside of class, usually via reading or lecture videos, and then online class time is used to do the harder work of assimilating that knowledge through strategies such as collaborative and peer learning, problem-solving, discussion or debates.  The key purpose of the flipped classroom is to engage students in active learning where there is a greater focus on students' application of conceptual knowledge rather than factual recall.

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Learning assessment methods

Final assessment is a discussion conducted online with the Faculty (formal indications)
Webex links will be comunicated to enroled students. The student under assessment will turn on microphone and webcam. At least another student will be connected as well, with webcam on and microphone off.

Further details on assessment method: 

Cell Biology and Human Genetics (9 credits):

  • Giachino C.: the identified student will answer 3 questions randomly extracted from a pool of open questions on the moodle exam platform. Test time: 10-15min/student.
  • Perroteau I.: the identified student will sort and discuss 3 questions randomly extracted from a pool of open and closed questions on moodle exam platform. Test time: 10-15min/student. 
  • Retta F.: the identified student will be interviewed on two topics of the cell biology program (CB part II). The questions will be randomly extracted from a pool of open and closed questions on moodle. Test time: 10-15min/student.

Molecular Genetics (2 credits):

  • Ceccarelli A.: Formative and summative assessments
  • Students will be subjected to formative assessment during the teaching and will provide a final Portfolio deonstrating the skills and competencies that have been achieved.
    • Types of exercises performed: During each unit homework will be assigned as teamwork, and will consist of assignments represented by short eassy/Problem solving, mind maps, flowcharts, question design.
    • group exercises (GA = GAssignment) - produced by teamwork, subject to peer-assessment, it can be inserted into the Portfolio at the discretion individual exercise (IA = IAssignment) - produced by the individual, may be subject to peer verification, it must be inserted into Portfolio.
    • Groups must perform and submit exercises in time for comments during the interim bout (according to the schedule set in each unit) , in order to get peer-to-peer (formative assessments) between the intermediate and the final meeting. During the meetings, the most relevant feedback is commented by the teacher and discussed with the class. At the end of each unit, students must carry out an individual assignment that will be included in the Portfolio and will be assessed for final grading
    • Peer assessment and summative assessment will be based on rubrics shared, discussed and agreed between the teacher and the students
    • Final assessment of the Portfolio of products that demonstrate the achievement of skills and competencies expected will be based on the appropriate rubric and on a final self-assessment document produced by the student.
    • For this purpose the performance tasks that will indicate achievement of the learning outcomes are:
      • factual knowledge: MC quizzes as self-assessment tools and question design for quiz test;
      • understanding: create hypotheses, design new instructive or revealing questions, elaborate learning strategies, construct concept maps, write short essays
    • During the course, at the end of each unit, and separately from the Portfolio, each member of each group will be asked to complete an evaluation form on the other members of the same group, which will be used by teachers to intercept general problems and for concerns of equity of commitment, and which will be kept confidential. At the end of each unit meetings will be arranged if required and at times not included in the course timetable to solve internal group problems.

 

  • Final CBG grade is calculated as weighted average of the independent assessments. Students will be informed if they passed or failed the exam by receiving their grade with automatic email message from Unito. Final grade are considered as accepted by default but can be deny by the student on Unito platform within 5 days of the comunication of the final grade. 

  • All marks are expressed as a value out of 30 points.
  • The final CBG grading is the weighted average of the marks of each lecturer.
  • Students with a weighted average of 30/30 and that have demonstrated high level of particpation to lectures and activities, both online and in class, can also be granted "30/30 cum lauda" as a commun decision of the 4 lecturers.
  • Final CBG grading, not each independent assessment, less than 18/30 will be considered as failed. Students with failed will have to sit again for the exam in one of the next sessions. 
  • The minutes with the final CBG mark is published at the end of each exam session.
  • Students within 5 days can deny their mark and sit again in one of the next sessions.
  • The web application through which the University manages the exams, from booking the registration to online filing of the results, is the ESSE3 platform.
  • In order to sit an exam, it is mandatory to register on ESSE3.
  • Instructions for students: log in to the portal UniTO.it and access the page MyUniTO. Then select the "Esami" entry "Exam sessions" (warning: not from the "Careers"> "Booklet")
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Support activities

Students with disorders that may affect learning (e.g. color blind students, visually impaired, hearing impaired, dyslexic or with physical disabilities) are encouraged to contact the lecturers to adapt learning materials, activities and testing methods.

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Program

At the end of the CB1 unit you are expected to be able to:
-Recall animal cell structures and functions
-Sketch an animal cell
-Recognize cell structures in optic and electron micrography
-Explain protein synthesis and sorting
-Describe the turnover of molecules and organelles
-Distinguish transport structures and mechanisms
-Arrange signal transduction pathways
-Relate basic experimental approaches in cell biology to scientific questions

Unit 01: Introduction to the cell 
Lectures (8 hrs)

- Cell membrane 
- Subcellular compartments: structure and functions
Student activities (4 hrs)
- Formative assessment (online)
- Critical thinking and inquiry skills: discussion on experimental study of cell structure and functions. 

Unit 02: Cell structures and functions 
Lectures (8 hrs)

- Protein synthesis and sorting to nucleus, mitochondria and peroxisomes
- The secretory pathway and vesicle-mediated transport
- Exocytosis, exosomes and microvesicles. Endocytosis, phagocytosis and macropinocytosis
- Transporters and channels
Student activities (4 hrs)
-Cognitive skills: Formative assessment on biological membranes (online) 
-Reasoning skills: Problem solving on molecular sorting
-Case study discussion: CFRT and Cystic fibrosis

Unit 03: Cell communication and signaling 
Lectures (8 hrs)

- Principle of cell communication
- G-protein coupled receptors - Heterotrimeric G protein-linked signal transduction - AC, PKA, PLC, PKC, PI3K
- Enzyme-linked receptors and cytokine receptors: RSTK, TKR, RPTPs, cytokine receptors
- Alternative signalings: adhesion receptors, protease-activated receptors and nuclear receptors.
Student activities (4 hrs)
- Cognitive skills: Formative assessment on cell communication and signalling
- Reasoning skills: Problem solving on signal transduction
- Problem-based discussion on cell communication and GPCR and enzyme-linked receptors signal transduction 
- Problem-based discussion on alternative signalings


 

Module delivery and organization

The Molecular Genetic Module is delivered as a flipped classroom

Teaching-

The class is divided into groups in the beginning, which remain the same for the duration of the course. The course is organized in 4 didactic Units Each unit is organized in:

  • 1) Opening Lecture (2hrs) - ask the questions, indicate the direction of reasoning, provide tips on where and how to get information, introducing the online content, introducing the assignments.
  • 2) 1 Intermediate meeting with groups (2hrs) to assess the progress made, investigate doubts, raise any other question
  • 3) Final meeting (2hrs) with the groups that conclude the initiated reasoning, comment the peer-assessments, and introduce the themes/tasks to be developed/accomplished for the portfolio
  • All llectures and meetings wil be held as online videoconferences. Instructions and links to join will be provided during the lectures and on the onnline material available through moodle platform

UNIT 1: DNA in living nuclei - structure, propagation and maintenance of genetic information- part 1: DNA in living nuclei

Established Goals:

  • Knowledge of the relationship between nucleic acid structure and function, Genetic information,
  • Knowledge of the relevance of nuclear architecture to gene function
  • Students will connect the above concepts to the concept of cell and organism health and diseases by understanding the role that DNA structure has in establishing the 3D architecture of nuclear chromatin, as well as the role that 3d chromatin architecture has in controlling a cell's genetic program and wellness.

Essential Questions:

  • Is information the same as "Order", i.e. opposite to "caos"?
  • Why is information needed by cells?
  • How many different types of information is the cell dealing with?
  • Is DNA carrying only genetic information?
  • Can the information contained in DNA be measured and how?
  • Is the shape in which DNA is packaged inside the nucleus information itself? If so could it be "Genetic"?
  • How many different things could in principle go wrong in a genetic system?
  • is every region of DNA carrying information a "gene"?
  • What are the possible uses of genes for a cell?
  • Are all diseases depending on genetic malfunctions?
  • Is there a common thread among the possible abnormalities in 3D genome organization that can become the most expected defect in the resulting diseases?

Students will understand that...

  • The dimension of the whole DNA moclecules and of the nuclei they will fit into are in a 10^9:1 ratio
  • DNA in a cell's nucleus must be organized into 3D or it won't fit+won't work
  • More than one type of information is stored into DNA
  • 3D distribution of information affects usage and is hence information intself
  • The 3D organization of DNA in nuclei is hyerarchical
  • The genome is modular in nature and blocks can be switched on/off/reshaped by very simple DNA-protein interactions
  • Nuclear chromosome territories are not random
  • Chromosome proximity is not random in living nuclei
  • 3D architecture can turn accidents to the DNA fiber into lethal situation

Students will know...

  • The structure of DNA
  • The common types of DNA manipulation
  • The defintion of gene, genome, functional element
  • The structure of prokaryotic and eukaryotic genes
  • The Encode Project
  • The chromatin and chromatin states
  • The nucleosomes
  • The epigenetic information
  • The mechansims deploying epigenetic information
  • The chromosome territories
  • The nuclear Compartments and TADs
  • The CTCF, cohesin and regulation of 3D architecture
  • The consequences of cell-type specific territories on chromosome structure

 

UNIT 2: DNA in living nuclei - structure, propagation and maintenance of genetic information- part 2: replication and repair of the genome

Established Goals:

  • Knowledge of the mechanis of the DNA synthesis process
  • Knowledge of the regulatory aspects od the geneome replication
  • Knowledge of the strategy of DNA repair pathways andof their functional connections to the DNA replication process
  • The students will connect the above concepts to the maintenance of the integrity of genetic informations as well as to the health of a cell and of an individual

Essential Questions:

  • How much of our lives depends upon ""base pairing""? It's just 2 vs 3 Hydrogen bonds....
  • Are information and recognition related concepts?
  • How relevant is recognition in living matter and in how many ways could we envisage recognition of genetic information?
  • How many different phenomena could ""base pairing"" mediate? (a rephrasing of the above)
  • Is the DNA repair strategy ancient or modern?
  • Could DNA repair be independent from the cell's metabolism (assume needed components are plentiful)
  • How many ways to make mechanisms interdipendent? or co-regulated?

Students will understand that...

  • The complementarity of bases is crucial to a wide range of phenomena
  • The genome needs to be replicated as a whole, yet ""completeness"" cannot be the only rule and DNA replication needs to be finely regulated
  • DNA replication aims at replicating all the information contained by DNA, including epigentic information
  • Replication of DNA and the reversibility of epigenetic information make replication an opportunity to reprogram cells
  • DNA damage can result from physiological proceses
  • DNA damage and genetic mutations are related but distinct phenomena
  • DNA damage results in wide variety of structures and the strategy to recognize them must be simple and sophisticated at the same time
  • DNA repair pathways differ mostly in their strategy and resemble each other in the mechanics of the repair process

Students will know ...

  • The structure of a replicon
  • The structure and function of prokaryotic and eukaryotic replisome
  • The function of the enzymes not part of the replisome and involved in the replicative process.
  • The mechanism of DNA synthesis
  • The structure of a replication bubble immediately after replisome has synthesized new strands
  • The types of replication origin
  • The protein complexes interacting with the origins at different stages
  • The recognition, licensing and firing phases
  • THe extra functions of the replisome
  • The replication foci
  • The replication factories
  • The types of DNA damage
  • The strategy to recognize different types od DNA damage
  • The strategies to repair DNA
  • The functional interacions between replication and repair

UNIT 3: copying and distributing genetic information to the gene expression machinery- part 1: Nucleus and RNA

Established Goals:

  • Knowledge fo the transcription of RNA
  • Kwonledge of the factors involved in the control of gene expression, both prokaryotic and eukaryotic
  • Knowledge of the relevance of RNA processing in controlling gene expression
  • Connect the critical steps in transcriptional and post-transcriptional control of gene expression to human diseases

Essential Questions:

  • Is the amount of information necessary to carry out transcription higher than that required to perform a whole genome replication?
  • Is double strandedness better than single strandedness?
  • Are exons between introns or introns between exons?
  • Where do genes come from?
  • How is the building blocks strategy relevant to the structure of a single gene/gene product?
  • Why do some types of cells process their transcripts while some others don't?

Students will understand that...

  • Single strandedness of RNA is a weakness as well as a strength
  • RNA molecules have properties and abilitites found in the protein kingdom, while proteins cannot behave like RNAs
  • RNA molecules are tools to perform sophisticated tasks
  • Tanscription is a regulated phenomenon
  • Endomembranes being obstacles to RNA usage in the cytoplasm offer a way to expand the coding potential of the genome and add further control on gene expression
  • Splicing is one of the most powerful tools to introduce meaningful mutations in the expressed genes
  • Genes evolved mainly through RNA splicing
  • TRanscriptional control of gene expression is articulated at several levels
  • DNA contains regulatory information distributed in various forms
  • Re-programming is not necessarily an automatic second passage on an epigenetically inactive genome

Students will know...

  • The RNA molecules
  • The mechanism of Transcription
  • The RNA polymerases (prok. and euk.)
  • The promoter
  • The core promoter
  • The enhancer/silencer
  • The termination signals
  • The transcription factors
  • The RNA processing mechanisms
  • The initiation complex and its related factors
  • The cotranscriptional processes involve din preRNA maturation
  • The l elements
  • The prokaryotic models of gene regulation
  • The eukaryotic levels of gene regulation
  • The evolutionary relevance of the splicing mechanism

UNIT 4: copying and distributing genetic information to the gene expression machinery- part 2: RNA in the cytoplasm

Established Goals:

  • Knowledge of the additional regulatory functions of some RNA molecules
  • Connect the regulatory RNAs to variations of human health and diseases and hypothesize possible uses as theraputic agents
  • Knowledge of the protein synthesis mechanism and of its involvement in human diseases
  • Knowledge of the genetic code and the rules that govern it
  • Knowledge of the existence of the mitochondrial genetic system
  • Connect the mitochendrial biochemical crossroad to each genetic system and relate possible abnormalities to correspoding biochemical defects in the patient's cells and organs

Essential Questions:

  • Is the statement "transcriptionnal control in mainly mediated by NucleicAcid/Protein interactions while post-transcriptional control is mainly mediated by by NucleicAcid/NucleicAcid interactions" correct? Why so or why not?
  • Is "non-coding" an meaningful definition for an RNA molecule?
  • Would a 4-letter genetic code (256 codons) be more useful?
  • Would extra codons only recognizable in an engineered situation of any use?
  • Is "damage" inherent to energy conversion?
  • Could "ageing speed" be a function of "living speed"?

Students will understand that...

  • RNAs can exploit their probing ability to mediate targeted assembly of regulatory structures on related targets
  • Systemtic transcription of apparently non-coding regions of the genome opens new possibilities every minute
  • The translational machinery provides a framework to use the genetic information at the highest possible digree of fidelity
  • The translational machinery offers an opportunity to regulate general aspects of the mRNA molecules, such as their half-life
  • Eukaryotic cells contain two genetic systems that are communicating with each other but only to some extent
  • The nuclear genome can affect the mitochondrial function(s) as much as the mitohondrial genome
  • Metabolic defects originating from mutations in the nuclear genome hitting the mitochondrial function will have some of the features of a "mitochondrial disease" even if not related to synthesis of ATP

Students will know...

  • The function fo non-coding RNAs of various size classes (miRNA, siRNA, lncRNA)
  • The mechanisms of RNA-mediated transcriptional and post-transcriptional regulation of gene expression
  • The mRNA silencing
  • The ribosome
  • The tRNAs
  • The aa-tRNA synthetases
  • The genetic code and its rules
  • The mechanism of mRNA translation and its regulation
  • The mitochondrial genetic system

 

 


Delivered according to the traditional classroom instructional strategy

Unit 04: Cell shape and motility 
Lectures (8 hrs)

- Cytoskeleton: Microfilaments, microtubules and intermediate filaments assembly and regulation
- Motor proteins of microfilaments and microtubules. Specialized structures: mitotic spindle, flagella, axon
- Cell-cell and cell-matrix adhesion and signaling 
- Motility processes and cell migration. Chemotaxis
Student activities (4 hrs)
- Cognitive, reasoning and communication skills: development and presentation of cooperative studies (group learning and group work at home) aimed at deeper understanding and contextualization in the medical field of the biological topics covered (4hrs, face to face).

Unit 05: Cell proliferation and survival
Lectures (10 hrs)
- Cell cycle regulation
- Mitosis and meiosis
- Accidental and programmed cell death
- Autophagy in cell survival and death
Student activities (4 hrs)
- Cognitive, reasoning and communication skills: development and presentation of cooperative studies (group learning and group work at home) aimed at deeper understanding and contextualization in the medical field of the biological topics covered (4hrs, face to face).

Unit 06: Cell differentiation
Lectures (6 hrs)

- Stem cells, cell differentiation, and development of multicellular organisms. Cell tracing 
- Nuclear reprogramming and induced pluripotent stem cells (iPSCs)
- Genetically modified animal models
Student activities (4 hrs)
- Cognitive, reasoning and communication skills: development and presentation of cooperative studies (group learning and group work at home) aimed at deeper understanding and contextualization in the medical field of the biological topics covered (4hrs, face to face).


Delivered according to the traditional classroom instructional strategy

Unit 01: Genetic heredity in eukaryotes
Lectures (8 hrs)
- Genetic stability and variability, Monofactorial characters and Mendel's laws
- Autosomal and X-linked characters
- Mitochondrial inheritance of diseases
- Herediting polygenic characters
- Molecular analysis of human loci
Student activities (4 hrs)
- Adaptive thinking and reasoning skills: Interpretation of family trees
- Reasoning skills: Problem solving on human disease inheritance

Unit 02: Mutations, population genetics and innovative therapies
Lectures (8 hrs)
- Point, chromosomal and genomic mutations
- Genetic variability and its modulation inside populations
- Immunogenetics and gene therapy
- Stem cell genetics and regenerative medicine
Student activities (4 hrs)
- Reasoning skills: problem solving on population genetics
- Critical thinking and inquiry skills: problem-based discussion on innovative therapies

Suggested readings and bibliography

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Required Text: ESSENTIAL CELL BIOLOGY, B. Alberts et al., 5th edition, W.W. Norton
Code discount for students of this course at www.wwnorton.co.uk:

  • 25% off print: BTU20
  • 10% off eBooks: EK10

Lecture slides, audio lecture recordings (as available), and primary research literature assigned by the instructors will be posted in moodle.

All course materials are copyrighted by the university and the individual instructors. Unauthorized distribution of these materials could violate the University Academic Integrity Policy and may subject you to disciplinary action.



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