Biomolecular Chemistry

Master in Industrial Chemistry and Introduction to Chemical Research

Master in Advance Nanoscience and Nanotechnology, Universitat Autònoma de Barcelona.

2020/2021

The project. Diagnostic tests for Sars-CoV-2

In light of the recent emergence of the Sars-CoV-2 worldwide, accurate and novel detection methods for the diagnosis of the disease are mandatory.

The objective of this subject is that at the end of the lectures you will be able to describe four different approaches for the diagnosis of the virus in different settings in the developed or in the developing world. This four approaches will be described in a written project which will be used for your assessment:

Approach 1. An approach for separating and preconcentrating SARS-CoV-2 virus from complex samples for further isolation of the virus.

Approach 2.  An RDT for the detection of the infection in low resource settings to screen out patients with requires strict surveillance and quarantine.

Approach 3. A test for quantifying the immunological response of the patients.

Approach 4. A confirmatory diagnosis of COVID in an outbreak setting and assessment of patient viral load as a predictor of outcome.

Instructions for the COVID Project

The main objective is to learn different methods based on Biomolecules (mainly antibodies and DNA based methods) by applying them in the detection of a target. The target selected is the SARS-CoV-2. Virus. Four different analytical challenges will be addressed, as described above. All these approaches will be discussed in the final project. The project will be developed step by step by meeting different milestones, and the lectures will help you out to achieve these milestones.

Introductory lesson of different approaches to detect communicable diseases

In this lesson you will find the different approaches in order to obtain a final diagnosis in the case of any infection disease, taking as a model SARS-CoV-2 virus. The link will be activated soon

Milestone 1

Find general information about SARS-CoV-2 virus infection and diseases. Write a summary about the virus that will help you to build up the introduction for the project. It will be the DELIVERABLE 1. More info.

Milestone 2

Find general information about the current diagnosis of the SARS-CoV-2 virus. It will be the DELIVERABLE 2.

Milestone 3. The final project

Describe the problem in an introduction (DELIVERABLE 1) as well as the current diagnostic of COVID (DELIVERABLE 2). Furthermore, describe, step by step, the development of each test procedure (approaches 1, 2, 3 and 4) and the protocol, for the detection of the biomarker related with SARS-CoV-2 Virus, taking into account: 

  • The production of the bioreagent (for instance, antibodies from the immunization to the purification) or, instead, the availability of commercial reagents. 
  • The format used for this specific biomarker as well as the platform.
  • The solid support and the immobilization strategy for the bioreagent. 
  • The labelling of the bioreagent, if needed.
  • The signal obtained for the quantification of the biomarker.

The theoretical lectures will help you out to fill all the final project, which will be the DELIVERABLE 3.

Assessment

The assessment of this part of the topic will be as follows,

i) Continuous assessment (40 % of the mark)

Virtual assessment activities proposed for the theoretical lectures as quizzes and as questions to solve in the forum.

QUIZ 1 QUIZ 2 QUIZ 3 QUIZ 4 QUIZ 5 QUIZ 6

The activities are designed to encourage the learning of specific skills. Activities must be delivered on time, on the specific place in a post open for that in the website. On the other hand, individual, autonomous work is required in order to reinforce the knowledge from reading and understanding the proposed reference books, web pages, tutorial videos or books that can be provided for specific topics. In order to carry out a self-assessment of learning, online multiple-choice tests will be proposed for each of the units, and their completion will also be considered in the assessment. 

ii) The COVID Project (60 % of the marks)

The Covid Project, including the three milestones: DELIVERABLE 1 (10 %), DELIVERABLE 2 (10 %) and DELIVERABLE 3 (40 %), (the final project).

Example of the assessment

Your marks will appear on the dashboard, in the GradeBook, as shown below:

General information

WHERE? Online teaching.

WHEN? Calendar for the online activities

HOW? General instructions for e-learning

MORE INFO. Check updated schedule for the master

GENERAL GUIDELINES. Click here to download

Theoretical Framework

Lesson 1. Introduction to bioanalytical chemistry

Classical Analytical Chemistry. Limitations of Classical Analytical Chemistry. Bioanalytical Chemistry Qualitative (Screening) Assays vs. Quantitative Assays

Lesson 2. Biomolecules and Biorecognition

Amino Acids, Peptides and Proteins. Antibodies. Enzymes. Nucleic Acids. Biorecognition: Enzyme/Substrate. Antigen/antibody. Hybridization. Other affinity interactions in nature. Strept(avidin), Protein A and G. Aptamers. Biomimetic recognition. The importance of water in biorecognition Biological buffers.

Lesson 3. Separation methods of biomolecules

Electrophoresis of proteins and DNA. Gel Electrophoresis (GE). SDS Polyacrylamide Gel Electrophoresis (SDS–PAGE). Southern, Northern and Western blot. Applications of Electrophoresis. Diagnosis of Genetic (Inherited) Disease. Paternity and forensic testing. DNA Sequencing. Diagnosis of infection diseases. Chromatography. Liquid Chromatography for Bioanalysis. Reversed Phase Liquid Chromatography (RP-LC). Ion Exchange Chromatography (IEC). Size Exclusion Chromatography (SEC). Affinity Chromatography. The special case of magnetic bioseparation.

Lesson 4. Production of bioreagents

Synthesis of short peptides and oligonucleotides.   Immunological Response. Production of monoclonal and polyclonal antibodies. Antibodies fragmentation. Synthesis the immunogens.    Purification of proteins from nature sources or cultures.     Purification of antibodies.

Lesson 5. Immunoassays

Classification. Antibody-Antigen Complex Formation. Assay Formats. Homogeneous and heterogeneous immunoassays. Labels in immunoassays: radioisotopes, fluorescence, chemiluminescent, enzymes. Enzyme Immunoassays: ELISA.     Immunoassay curve fitting.

Lesson 6. DNA analysis and amplification

Hybridization reaction of DNA. DNA amplification. PCR (polymerase chain reaction). The Principle of PCR. Reagents for PCR. Real-Time PCR (Q-PCR). Reverse Transcription PCR (RT-PCR)

Lesson 7. Rapid and screening methods

RDTs (rapid diagnostic test). Immunochromatography and lateral flow assays. Home pregnancy test.  Agglutination techniques.   ABO typing for blood group determination.      Biosensors. Glucose biosensor.    Statistical in screening methods. Cut-off determination. Binary classification test.  Problems and exercises (update version)

Lesson 8. Immobilization and labeling of biomolecules.

Solid supports in bioanalytical chemistry. Immobilization strategies of biomolecules in solid supports. Non-specific adsorption. Blocking reagents.      Labeling of biomolecules: enzymes, fluorophores, nanoparticles, QDs, biotin. Signal amplification strategies.

Lesson 9. Nanomaterials in Bioscience

Biorecognition with biologically-modified quantum dots, carbon nanotubes, metal and magnetic
nanoparticle: medical diagnosis, nanomedicine and bioanalysis.

Multimedia

Selected videos and multimedia

Bibliography

– Bioanalytical Chemistry. Susan R. Mikkelsen & Eduardo Cortón. Wiley-interscience. 2004.
– Principles and Techniques of Biochemistry and Molecular Biology. 6 ª ed. Edited by Keith Wilson & John Walker. Cambridge University Press. 2006.
– Bioanalytical Chemistry. Andreas Manz. Nicole Pamme. Dimitri lossifidis. Imperial College Press, 2004..
– Principles and Practice of Bioanalysis. Edited by Richard F. Venn. Taylor & Francis, 2000.

Bibliography. The basic

– David L. Nelson, Michel M. Cox. ‘Lehninger Principios de Bioquímica’. 4ª ed. Ediciones Omega. 2006.
– L. Stryer, Jeremy M. Berg, John L. Tymocxko. Bioquímica. 5 ª ed. Editorial Reverté. 2003.
– Mary K. Campbell, Shawn O. Farrell. Bioquímica. 4 ª ed. Editorial Thomsom. 2004.

– Skoog, Holler i Niemen. “Principios de Análisis Instrumental” 5ª edició. Ed. Mc. Graw Hill. 2001.
– Skoog, West, Holler i Crouch “Fundamentos de Química Analítica” 8ª edició. Ed. Thomsom, 2005.
– Daniel C. Harris “Análisis químico cuantitativo”. 2ª ed (5ª en Ingles), Editorial Reverte 2001.

Other suggested bibliography

– ‘Bioquimica. Técnicas y Métodos’. Pilar Roca, Jordi Oliver y Ana Mª Rodríguez. Editorial Hélice. 2003.
– Bryan L. Williams, Keith Wilson. Principios y Técnicas de Bioquímica experimental. Ediciones Omega, 1981.
– J.M. García Segura, J.G. Gavilanes, A. Martínez del Pozo, F. Montero, M. Oñaderra, F. Vivanco. Técnicas instrumentales de análisis en Bioquímica. Editorial Síntesis, 2002.
– D.J. Holme, H. Peck. Analytical Biochemistry. 3rd edition. Prentice Hall, 1998.
– Reiner Wetermeier and Tom Naven. Proteomics in Practice: A Laboratory Manual of Proteome Analysis, Wiley-VCH Verlag-GmbH,. Weinheim, 2002.
– Rodney F. Boyer, Modern Experimental Biochemistry (Third Edition) Benjamin/Cummings, San Francisco, 2000.
– Handbook of Experimental Immunology. Vol. 1. Weir DM, ed. Oxford: Blackwell Scientific Publications, 1986.
– Rodney F. Boyer, Biochemistry Laboratory. Modern Theory and Techniques. Publisher: Benjamin Cummings. 2006.
– Jeremy W Dale and Malcom von Schantz. From Genes to Genomes: Concepts and Applications of DNA Technology. John Wiley & Sons, Ltd. 2002
– Sample Preparation Techniques in Analytical Chemistry. Somenath Mitra, ed. Wiley-Interscience: Hoboken, NJ, 2003.Edit