PřF:Bi6721c Spec.Meth.Microorg.Anal.I.-pr. - Course Information

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).
In-person direct teaching

Teacher(s)

doc. Mgr. Pavel Dvořák, Ph.D. (seminar tutor)
Mgr. Barbora Jankovičová (seminar tutor)
Mgr. Matúš Pešta (seminar tutor)

Guaranteed by

doc. Mgr. Pavel Dvořák, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: Ing. Jiřina Kučerová, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. )
Prerequisite for registration of the lab practice is parallel enrollment in the course Special Methods of Microorganisms Analysis (Bi6721).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 10/10, only registered with preference (fields directly associated with the programme): 0/10

fields of study / plans the course is directly associated with

there are 6 fields of study the course is directly associated with, display

Course objectives

The aim of this practical course is to familiarise students, through two consecutive blocks of 3 + 3 sessions (individual sessions are organised once every 14 days throughout the semester), with the procedures for:

(A) the identification and characterisation of microorganisms using Polymerase Chain Reaction (PCR) and related bioinformatic (primer design, sequence data analysis) and experimental methods (the PCR reaction itself, separation and purification of DNA molecules, preparation for sequencing), and

(B) the cloning of a microbial gene using PCR and restriction digestion into a plasmid, its heterologous expression in a surrogate host, and the purification of the resulting overproduced protein using affinity chromatography.

Learning outcomes

Throughout the course, students will demonstrate the practical ability to perform the identification of unknown microorganisms using molecular biology and bioinformatic methods, as well as a knowledge of microbial gene cloning, their expression, and the purification of the resulting proteins. The main outcomes of the practical sessions are two detailed protocols, including a description of the methods, results, conclusions, and discussion, for which students will receive high-quality feedback from the lecturers with individual friendly attitude.

Syllabus

Session 1: Preparation of bacterial lysates from cultures of Escherichia coli and an unknown bacterium designated for identification, PCR design, and the execution of end-point PCR – Amplification of two specific genes, including the gene for 16S rRNA.

Session 2: Electrophoresis and purification of PCR products, evaluation of PCR success, and preparation of the purified DNA for sequencing.

Session 3: Theoretical session on bioinformatic methods – Computational analysis of sequencing results using the Benchling programme, demonstration of primer design for the amplification of a species-specific gene (Session 1) and for cloning a gene into a plasmid vector (Session 4).

Session 4: Amplification of a selected gene using PCR with primers from Session 3, restriction digestion of the PCR product and the plasmid vector, and ligation of the PCR product into the plasmid.

Session 5: Verification of the successful cloning of the PCR fragment into the plasmid, transformation of Escherichia coli BL21 (DE3) with the plasmid construct, and verification of successful transformation.

Session 6: Cultivation of the transformed E. coli in liquid medium, expression of the cloned gene, and purification of the recombinant protein using affinity chromatography.

Literature

• Green, M.R., Sambrook, F. Molecular Cloning. A Laboratory Manual. 4th ed. Cold Spring Harbor Laboratory Press. 2012

  ​Kopecká, J., Bartoš, M. Speciální metody analýzy mikroorganizmů I, návody ke cvičení​, 2014

Teaching methods

The practical sessions are held during the spring semester once every 14 days for a double time period (i.e., a double block of hours). The first three sessions will be conducted in Czech, and the subsequent three sessions will be conducted in English. This will give students the opportunity to attend part of the instruction in a foreign language and improve their knowledge of specialised English terminology.

During the practical sessions, students work in pairs, and each pair processes their own sample. The textual assignment for each session, including the procedure, is made available to the students in advance. Students summarise and evaluate the results of their experiments in a clear and concise manner within their protocols. The protocols are drafted according to specific instructions (information provided in the first session and during the lecture). In each protocol, the student describes, compares, analyses, evaluates, and discusses their own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course, for the preparation of protocols, and for a brief discussion with the lecture about the prepared protocols.

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7430c Molecular biotechnology - practical course

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught every week.
General note: Předmět se doporučuje zapsat ve 2. semestru společně s přednáškou, případně pak ve 4. semestru.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

• Enrolment Statistics (recent)
  
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