Cellular and Molecular Biology Techniques and Applications in Marine Sciences

Code:

RM03

Acronym:

TABCMCM

Keywords
Classification	Keyword
OFICIAL	Marine Sciences

Instance: 2022/2023 - 1S (of 12-09-2022 to 10-02-2023)

Active?	Yes
Responsible unit:	Microscopy
Course/CS Responsible:	Master Degree in Marine Sciences - Marine Resources

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
MCMRM	16	Oficial Plan 2018	1	-	5	50	135

Teaching language

Portuguese and english
Obs.: Em inglês se necessário | In English if necessary

Objectives

To get the students to be more aware of various types of techniques used to analyze biological samples in cellular and molecular biology, emphasizing aquatic animals.

Reminding and clarifying students about the theoretical principles that underlie each technique, as well as providing protocols and exemplifying some of its most common applications in biology.

Allow the applicant's to get into a learning experience of "know-how" with regard to selected techniques used in molecular and cellular biology.

Learning outcomes and competences

At the end of classes, the student must show that he has knowledge, understanding, implementation capacity and competence in the areas relating to various techniques, cytological, histological (microscopy, optics, electronics and fluorescence), cytometry, cell culture and molecular (as primer design and qtRT-PCR).

One of the learning outputs is also to increase the experience of working in a group for the resolution of problems.

Working method

Presencial

Program

NECROPSY, COLLECTION, PROCESSING AND ANALYSIS OF BIOLOGICAL SAMPLES.

CULTURE OF CELLS: Introduction to the basic principles. Equipment. Preparation of reagents and equipment. Primary cell cultures. Subcultures and cell lines. Contamination. Cryopreservation. Quantification. Applications. 2D vs. 3D cultures.

PROCESSING FOR MICROSCOPY OPTICS: THE COLLECTION In BLADE: Introduction. Dissection and collection of samples. Criofixacao. Fixation and decalcification. Dehydration. Diaphanization. Impregnation and inclusion. Sectioning.

SAMPLE COLLECTION AND PROCESSING FOR MICROSCOPY ELETRÓNICA: Introduction. Dissection and collection of samples. Processing of the tissue. Ultramicrotomia. Coloring and hallmarking. Criotecnicas. Observation under the microscope. Applications.

COLORING TECHNIQUES IN MICROSCOPY OPTICS: Introduction to theory of coloration. Description of some of the most used techniques in histology: Hemateina & Eosin. Argentum Impregnation: method of Bielschowsky's for nerve fibers and axons; Gomori Method to reticular fibers. Masson trichrome for collagen fibrils. Stainings for lipids. Nissl Stainings for the nervous tissue. Weigert Staining for elastic fibers.

HISTOQUÍMICA: Introduction. Preparation of the tissue. Histochemical Methods. Qualitative versus quantitative Analysis. Applications.

IMUNOHISTOQUÍMICA: Introduction. Production of antibodies. Preparation of the tissue. Direct and indirect Method. Visualization of the final products of the reaction (optical microscopy and electronic). Qualitative versus quantitative Analysis. Applications.

IF-POSITIVE CELLS: Introduction. Antigens. Methods for preservation of the antigen. Selection of antibodies. Procedure. Applications. Introduction to confocal microscopy.

TECHNIQUES CITOLÓGICAS: Introduction. General Principles of cytology. Handling of samples. Preparation of the samples. Staining of cytological samples. Cytological Observation. Applications.

GENO/CYTOTOXICITY TESTS: the comet assay.

STEREOLOGY: Introduction. The importance of quantification. Target Parameters. Measures in organs, cells and organelles.

INTRODUCTION TO MOLECULAR METHODS: DNA. RNA. Transcription. Translation. Genetic Code. Protein.

HIBRIDIZAÇÃO IN-SITU: Introduction. Types of probes. Preparation of tissue and pre-treatment of the sample. Revelation of hybrids. Aib and modes of observation. Qualitative versus quantitative Analysis. Applications.

FLOW CYTOMETRY: Pincipios and applications.

WESTERN BLOT: Technique, Theory, Practices, and Trouble Shooting

THEORETICAL CONCEPTS ABOUT MOLECULAR BIOLOGY: Structure of the gene, exons, introns, promoters, regulatory mechanisms. Molecular Evolution, homology/analogy. Molecular biology Applications - examples.

BIOINFORMÁTICA/ LAB RNA: Bioinformatics: introductory Notes; GenBank and Ensembl; Resources; genomic Alignments, conserved Regions; Phylogeny; practical Exercise. Lab RNA: introductory Notes; Extraction of RNA concentration, quality assessment, synthesis of cDNA.

REAL TIME PCR: introductory Notes on the basic principles of the technique. Laboratory Exercise with the RT-PCR. Discussion of the results. Alternatives: advanced methods of molecular expression.

HEMATOLOGY TECHNIQUES: Brief introduction to Princíples and Applications.

THE END

Mandatory literature

Andreas Hofmann, Samuel Clokie; Wilson and Walker's Principles and Techniques of Biochemistry and Molecular Biology (8th Edition), Cambridge University Press, 2018. ISBN: 131661476X
John Cook, Phil Warren; Cellular Pathology, third edition: An Introduction to Techniques and Applications , Scion Publishing Ltd., 2015. ISBN: 1907904352
Kim S Suvarna, Christopher Layton, John D. Bancrof;; Bancroft's Theory and Practice of Histological Techniques (8th Edition), Elsevier, 2018. ISBN: 0702068640
Richard W. Burry; Immunocytochemistry: A Practical Guide for Biomedical Research , Springer, 2010. ISBN: 1441913033
R. Ian Freshney and Amanda Capes-Davis; Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications (8th Edition), Wiley-Blackwell, 2021. ISBN: 1119513014
Sarah Maddocks, Rowena Jenkins; Understanding PCR: A Practical Bench (1st Edition), Academic Press, 2016. ISBN: 0128026839

Complementary Bibliography

Material distribuído pelos docentes.
van Pelt-Verkuil, E., van Belkum, A, Hays, JP; • Principles and Technical Aspects of PCR Amplification, Springer, 2008. ISBN: 9789048175796
Christine Goetz, Jody Bonnevier, Christopher Hammerbeck; Flow Cytometry Basics for the Non-Expert, Springer, 2018. ISBN: 978-3319980706

Teaching methods and learning activities

Lectures
Practical Training*

*Short reports or questionnaires may be requested.

keywords

Natural sciences > Biological sciences > Biology > Molecular biology
Natural sciences > Biological sciences > Biology > Cell biology

Evaluation Type

Distributed evaluation with final exam

Assessment Components

Designation	Weight (%)
Exame	70,00
Trabalho escrito	30,00
Total:	100,00

Amount of time allocated to each course unit

Designation	Time (hours)
Elaboração de projeto	10,00
Estudo autónomo	75,00
Frequência das aulas	50,00
Trabalho escrito
Total:	135,00

Eligibility for exams

According to the Law and Regulations of UPorto and ICBAS.

It is compulsory to attend 3/4 of the lectured classes.

Calculation formula of final grade

Final Grade = Final Exam Grade x 0.70 x + Project Grade x 0.30 + Bonus

The exam and project grades are given on a scale from 0 to 20 points.

Final Exam - Multiple choice test. It contains questions that derive from the teaching-learning obtained in practical classes.

Project - As described in Examinations or Special Assignments.

Bonus - Students who present the Project in English (written text and oral presentation) will have a bonus of up to 1 value.

The final classification is from 0 to 20 values, rounded up to the unit.

Examinations or Special Assignments

Project - Oral Presentation 1 a web page devoted to a detailed presentation of the techniques used during classes (cellular or molecular biology), in its application in the field of marine sciences.

One practical example of its application, based on a good reference 1 original article published in Scopus indexed international journal should be included.

The work is done in groups of 4 to 6 students (no more than 4 groups). The groups CAN NOT present projects based on the same technique, and so there must be an effort of inter-group coordination.

On the day of the presentation (a "guided tour of the page"), those who present the protocol and those who present and justify the choice of the application example will be chosen by lot. All elements (and especially those that did not present) can be asked to answer questions related to work.

Note: Overcoming the presentation time of the project (maximum of 15 minutes) will negatively impact on the final grade.

Classification improvement

Conducting a new final exam, with no improvement in the continuous component (except if the student attends the unit again, in the following academic year).

Observations

Guest speakers: the curricular unit can annually invite some speakers, present advances in selected technical topics, in addition to being able to participate in practical teaching.

Doctor Célia Cristina Lopes and Doctoral student and MSc Fernanda Cristina Rodrigues Malhão are part of the UC teaching team.