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).

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: 11/10, 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 the practical course is to acquaint students with the method of isolation of plasmid and genomic DNA of bacteria using a kit, with the design of oligonucleotide primers and preparation of polymerase chain reaction (end-point and quantitative real-time PCR), with the method of control gel electrophoresis, sequence analysis, and with the purification of the foreign protein from the host bacterium by affinity chromatography.

Learning outcomes

At the end of this course, the students should be able to use practically the microbial DNA isolation protocol, the method of polymerase chain reaction, sequence analysis, and the gel electrophoresis method.

Syllabus

• 1. Preparation of bacterial lysates from cultures of Pseudomonas putida and Escherichia coli.
• 2. Amplification of four specific genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 9. Polymerase chain reaction by system end-point, gel electrophoresis.
• 10. Real-time PCR with DNA sample from cytomegalovirus.
• 11. Purification of a recombinant protein from Escherichia coli 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 practice takes place once in 14 days. Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v  the first practice and lecture). In the protocols students describe, compare, analyze, evaluated and discuss 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.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. Pavel Dvořák, Ph.D. (seminar tutor)
Mgr. Barbora Burýšková (seminar tutor)
Mgr. Barbora Popelářová (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

Timetable

Mon 19. 2. to Sun 26. 5. Mon 13:00–18:50 E25/119

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: 4/10, only registered: 0/10, 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 the practical course is to acquaint students with the method of isolation of plasmid and genomic DNA of bacteria using a kit, with the design of oligonucleotide primers and preparation of polymerase chain reaction (end-point and quantitative real-time PCR), with the method of control gel electrophoresis, sequence analysis, and with the purification of the foreign protein from the host bacterium by affinity chromatography.

Learning outcomes

At the end of this course, the students should be able to use practically the microbial DNA isolation protocol, the method of polymerase chain reaction, sequence analysis, and the gel electrophoresis method.

Syllabus

• 1. Preparation of bacterial lysates from cultures of Pseudomonas putida and Escherichia coli.
• 2. Amplification of four specific genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 9. Polymerase chain reaction by system end-point, gel electrophoresis.
• 10. Real-time PCR with DNA sample from cytomegalovirus.
• 11. Purification of a recombinant protein from Escherichia coli 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 practice takes place once in 14 days. Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v  the first practice and lecture). In the protocols students describe, compare, analyze, evaluated and discuss 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)

Study Materials
The course is taught annually.
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.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. Pavel Dvořák, Ph.D. (seminar tutor)
Mgr. Barbora Burýšková (seminar tutor)
Mgr. Barbora Popelářová (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

Timetable

Mon 13:00–18:50 E25/119

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: 0/10, 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 the practical course is to acquaint students with the method of isolation of plasmid and genomic DNA of bacteria using a kit, with the design of oligonucleotide primers and preparation of polymerase chain reaction (end-point and quantitative real-time PCR), with the method of control gel electrophoresis, sequence analysis, and with the purification of the foreign protein from the host bacterium by affinity chromatography.

Learning outcomes

At the end of this course, the students should be able to use practically the microbial DNA isolation protocol, the method of polymerase chain reaction, sequence analysis, and the gel electrophoresis method.

Syllabus

• 1. Preparation of bacterial lysates from cultures of Pseudomonas putida and Escherichia coli.
• 2. Amplification of four specific genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 9. Polymerase chain reaction by system end-point, gel electrophoresis.
• 10. Real-time PCR with DNA sample from cytomegalovirus.
• 11. Purification of a recombinant protein from Escherichia coli 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 practice takes place once in 14 days. Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v  the first practice and lecture). In the protocols students describe, compare, analyze, evaluated and discuss 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
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
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.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. Pavel Dvořák, Ph.D. (seminar tutor)
Mgr. Barbora Burýšková (seminar tutor)
Mgr. Barbora Popelářová (seminar tutor)
Mgr. Jozef Kováč (assistant)

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

Timetable

Tue 25. 5. 13:00–17:00 E25/111, Wed 26. 5. 8:00–12:00 E25/111, Mon 31. 5. 13:00–17:00 E25/111, Tue 1. 6. 8:00–12:00 E25/111

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
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 8 student(s).
Current registration and enrolment status: enrolled: 0/8, only registered: 0/8, only registered with preference (fields directly associated with the programme): 0/8

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 the practical course is to make students familiar with: (i) the method of plasmid and genomic bacterial DNA isolation using kits, (ii) with PCR reaction preparation, and (iii) with the control gel electrophoresis.

Learning outcomes

At the end of this course, the students should be able to use practically the microbial DNA isolation protocol, the method of polymerase chain reaction, and the gel electrophoresis method.

Syllabus

• 1. Preparation of bacterial lysates from cultures of Pseudomonas putida and Escherichia coli.
• 2. Amplification of four specific genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Isolation of the genomic DNA from the sample with Chlamydia trachomatis.
• 9. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 10. Polymerase chain reaction by system end-point, gel electrophoresis.
• 11. Real-time PCR with DNA sample from cytomegalovirus.
• 12. Purification of a recombinant protein from Escherichia coli 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

Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v the first practise and lecture). In the protocols students describe, compare, analyze, evaluated and discuss 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
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
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.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. Pavel Dvořák, Ph.D. (seminar tutor)
Mgr. Barbora Burýšková (seminar tutor)
Mgr. Barbora Popelářová (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

Timetable

Mon 13:00–15:50 E25/111

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
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: 0/10, 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 the practical course is to make students familiar with: (i) the method of plasmid and genomic bacterial DNA isolation using kits, (ii) with PCR reaction preparation, and (iii) with the control gel electrophoresis.

Learning outcomes

At the end of this course, the students should be able to use practically the microbial DNA isolation protocol, the method of polymerase chain reaction, and the gel electrophoresis method.

Syllabus

• 1. Preparation of bacterial lysates from cultures of Pseudomonas putida and Escherichia coli.
• 2. Amplification of four specific genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Isolation of the genomic DNA from the sample with Chlamydia trachomatis.
• 9. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 10. Polymerase chain reaction by system end-point, gel electrophoresis.
• 11. Real-time PCR with DNA sample from cytomegalovirus.
• 12. Purification of a recombinant protein from Escherichia coli 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

Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v the first practise and lecture). In the protocols students describe, compare, analyze, evaluated and discuss 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
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
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.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. Pavel Dvořák, Ph.D. (seminar tutor)
Mgr. Barbora Burýšková (assistant)

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

Timetable

Mon 18. 2. to Fri 17. 5. Mon 14:00–16:50 E25/111

Prerequisites (in Czech)

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )

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 16 student(s).
Current registration and enrolment status: enrolled: 0/16, only registered: 0/16, only registered with preference (fields directly associated with the programme): 0/16

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 the practical course is to make students familiar with: (i) the method of plasmid and genomic bacterial DNA isolation using kits, (ii) with PCR reaction preparation, and (iii) with the control gel electrophoresis.

Learning outcomes

At the end of this course, the students should be able to use practically the microbial DNA isolation protocol, the method of polymerase chain reaction, and the gel electrophoresis method.

Syllabus

• 1. Preparation of bacterial lysates from cultures of Pseudomonas putida and Escherichia coli.
• 2. Amplification of four specific genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Isolation of the genomic DNA from the sample with Chlamydia trachomatis.
• 9. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 10. Polymerase chain reaction by system end-point, gel electrophoresis.
• 11. Real-time PCR with DNA sample from Chlamydia trachomatis.
• 12. Delivery of filled in lab protocols, discussion.

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

Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v the first practise and lecture). In the protocols students describe, compare, analyze, evaluated and discuss own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Milan Bartoš, Ph.D. (seminar tutor)
Bc. Michael Kobza (assistant)

Guaranteed by

Mgr. Iva Buriánková, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Milan Bartoš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Mon 14:00–16:50 E25/111

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

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 24 student(s).
Current registration and enrolment status: enrolled: 0/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

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 the practical course is to familiarize students with the method of DNA isolation using kit, preparation of reaction to PCR and control gel electrophoresis from samples of bacteria and yeasts.

Learning outcomes

At the end of this course, the students should be able practically use the isolation of DNA, the method of polymerase chain reaction and gel electrophoresis from samples of bacterial and yeast cells.

Syllabus

• 1. Příprava bakteriálních lyzátů z kultur čeledi Pasteurellaceae.
• 2. Amplification of three genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Isolation of the genomic DNA from the sample with Chlamydia trachomatis.
• 9. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 10. Polymerase chain reaction by system end-point, gel electrophoresis.
• 11. Real-time PCR - Chlamydia trachomatis.
• 12. Isolation DNA from yeasts (phenol-chloroform extraction), gel electrophoresis.
• 13. PCR of the ITS region for differentiation complex Saccharomyces sensu stricto, gelová electrophoresis.
• 14. Cleavage of the PCR products by restriction endonucleasis, gel electrophoresis.

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

Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v the first practise and lecture). In the protocols students describe, compare, analyze, evaluated and discuss own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Milan Bartoš, Ph.D. (seminar tutor)
Mgr. Gabriela Rotková, Ph.D. (seminar tutor)
Bc. Michael Kobza (assistant)

Guaranteed by

prof. RNDr. Zdeněk Hubálek, DrSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Milan Bartoš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable of Seminar Groups

Bi6721c/01: Mon 20. 2. to Mon 22. 5. Tue 13:00–15:50 E25/111, M. Bartoš, G. Rotková
Bi6721c/02: Mon 20. 2. to Mon 22. 5. Tue 16:00–18:50 E25/111, M. Bartoš, G. Rotková

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

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 24 student(s).
Current registration and enrolment status: enrolled: 0/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

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

At the end of this course, the students should be able practically use the isolation of DNA, the method of polymerase chain reaction and gel electrophoresis from samples of bacterial and yeast cells.

Syllabus

• 1. Příprava bakteriálních lyzátů z kultur čeledi Pasteurellaceae.
• 2. Amplification of three genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Isolation of the genomic DNA from the sample with Chlamydia trachomatis.
• 9. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 10. Polymerase chain reaction by system end-point, gel electrophoresis.
• 11. Real-time PCR - Chlamydia trachomatis.
• 12. Isolation DNA from yeasts (phenol-chloroform extraction), gel electrophoresis.
• 13. PCR of the ITS region for differentiation complex Saccharomyces sensu stricto, gelová electrophoresis.
• 14. Cleavage of the PCR products by restriction endonucleasis, gel electrophoresis.

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

Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v the first practise and lecture). In the protocols students describe, compare, analyze, evaluated and discuss own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Milan Bartoš, Ph.D. (seminar tutor)
Mgr. Gabriela Rotková, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Zdeněk Hubálek, DrSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Milan Bartoš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable of Seminar Groups

Bi6721c/01: Mon 9:00–11:50 E25/111, M. Bartoš, G. Rotková
Bi6721c/02: Mon 12:00–14:50 E25/111, M. Bartoš, G. Rotková

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

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 24 student(s).
Current registration and enrolment status: enrolled: 0/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

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

At the end of this course, the students should be able practically use the isolation of DNA, the method of polymerase chain reaction and gel electrophoresis from samples of bacterial and yeast cells.

Syllabus

• 1. Příprava bakteriálních lyzátů z kultur čeledi Pasteurellaceae.
• 2. Amplification of three genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Isolation of the genomic DNA from the sample with Chlamydia trachomatis.
• 9. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 10. Polymerase chain reaction by system end-point, gel electrophoresis.
• 11. Real-time PCR - Chlamydia trachomatis.
• 12. Isolation DNA from yeasts (phenol-chloroform extraction), gel electrophoresis.
• 13. PCR of the ITS region for differentiation complex Saccharomyces sensu stricto, gelová electrophoresis.
• 14. Cleavage of the PCR products by restriction endonucleasis, gel electrophoresis.

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

Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v the first practise and lecture). In the protocols students describe, compare, analyze, evaluated and discuss own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Milan Bartoš, Ph.D. (seminar tutor), prof. RNDr. Zdeněk Hubálek, DrSc. (deputy)
Mgr. Jana Čmielová, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Zdeněk Hubálek, DrSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Milan Bartoš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 16:00–17:50 E25/111

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

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 24 student(s).
Current registration and enrolment status: enrolled: 0/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

fields of study / plans the course is directly associated with

• Special Biology (programme PřF, B-EXB)
• Special Biology (programme PřF, B-EXB, specialization Mikrobiology a Molecular Biotechnology)
• Special Biology (programme PřF, N-EXB)
• Special Biology (programme PřF, N-EXB, specialization Mikrobiologie a molekulární biotechnologie)

Course objectives

At the end of this course, the students should be able practically use the isolation of DNA, the method of polymerase chain reaction and gel electrophoresis from samples of bacterial and yeast cells.

Syllabus

• 1. Příprava bakteriálních lyzátů z kultur čeledi Pasteurellaceae.
• 2. Amplification of three genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Isolation of the genomic DNA from the sample with Chlamydia trachomatis.
• 9. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 10. Polymerase chain reaction by system end-point, gel electrophoresis.
• 11. Real-time PCR - Chlamydia trachomatis.
• 12. Isolation DNA from yeasts (phenol-chloroform extraction), gel electrophoresis.
• 13. PCR of the ITS region for differentiation complex Saccharomyces sensu stricto, gelová electrophoresis.
• 14. Cleavage of the PCR products by restriction endonucleasis, gel electrophoresis.

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

Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v the first practise and lecture). In the protocols students describe, compare, analyze, evaluated and discuss own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Timetable

Mon 8:00–13:50 Bpb,02012

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

At the end of this course, the students should be able practically use the method of polymerase chain reaction for the identification of bacteria.

Syllabus

• 1. Safety of work in microbiology laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria.
• 2. Preparation of Salmonella Typhimurium LB5000 cells for isolation of bacterial DNA. Cell lysis.
• 3. DNA deproteination using phenol extraction. Precipitation of DNA with ethanol.
• 4. Estimation of DNA integrity using agarose gel electrophoresis of isolated DNA. DNA visualisation and gel documentation.
• 5. Estimation of DNA concentration and purity. Preparation of DNA in concentration suitable for PCR.
• 6. The work flow in PCR laboratory. Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. PCR reaction.
• 7. Detection of PCR product using agarose gel electrophoresis.
• 8. Estimation of amplicon length using known standards.
• 9. Preparation of PCR mixture from trude cell lysates. Positive and negative controls. PCR and detection of PCR produkt.
• 10.Imunomagnetic separation (IMS) of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR) with cells Salmonella. Estimation of PCR sensitivity.
• 11.I PCR products detection using agarose gel electropjoresis.
• 12. and 13. Identification of Salmonella cells in unknown sample using PCR.
• 14. Evaluation of protocols.Test.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Teaching methods

Each student works independently and processes his or her own sample during the laboratory course. The results of their experiments must be evaluated in a protocol. The protocols (4 in number) are elaborated in the form of a poster according to the following scheme: Introduction, Aim of work, Material and methods, Results, Discussion, Conclusion. In the protocol each student describes, compares, analyses, evaluates, and discusses his or her own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols (4). In the course of the credit exercise, each student has to identify target bacteria in an unknown sample using the PCR method.

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Timetable of Seminar Groups

Bi6721c/01: Mon 10:00–12:50 Bpb,02012, B. Rittich, A. Španová
Bi6721c/02: Mon 13:00–15:50 Bpb,02012, B. Rittich, A. Španová

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

At the end of this course, the students should be able practically use the method of polymerase chain reaction for the identification of bacteria.

Syllabus

• 1. Safety of work in microbiology laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria.
• 2. Preparation of Salmonella Typhimurium LB5000 cells for isolation of bacterial DNA. Cell lysis.
• 3. DNA deproteination using phenol extraction. Precipitation of DNA with ethanol.
• 4. Estimation of DNA integrity using agarose gel electrophoresis of isolated DNA. DNA visualisation and gel documentation.
• 5. Estimation of DNA concentration and purity. Preparation of DNA in concentration suitable for PCR.
• 6. The work flow in PCR laboratory. Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. PCR reaction.
• 7. Detection of PCR product using agarose gel electrophoresis.
• 8. Estimation of amplicon length using known standards.
• 9. Preparation of PCR mixture from trude cell lysates. Positive and negative controls. PCR and detection of PCR produkt.
• 10.Imunomagnetic separation (IMS) of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR) with cells Salmonella. Estimation of PCR sensitivity.
• 11.I PCR products detection using agarose gel electropjoresis.
• 12. and 13. Identification of Salmonella cells in unknown sample using PCR.
• 14. Evaluation of protocols.Test.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Teaching methods

Each student works independently and processes his or her own sample during the laboratory course. The results of their experiments must be evaluated in a protocol. The protocols (4 in number) are elaborated in the form of a poster according to the following scheme: Introduction, Aim of work, Material and methods, Results, Discussion, Conclusion. In the protocol each student describes, compares, analyses, evaluates, and discusses his or her own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols (4). In the course of the credit exercise, each student has to identify target bacteria in an unknown sample using the PCR method.

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Timetable of Seminar Groups

Bi6721c/01: Wed 8:00–10:50 Bpb,02012, B. Rittich, A. Španová
Bi6721c/02: Wed 11:00–13:50 Bpb,02012, B. Rittich, A. Španová

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is for the students which will know to performe the basic noncultivation microbiological method polymerase chain reaction.

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

Safety of work in mikrobiology laboratory. Basic procedures with DNA work: isolation and purification of bacterial DNA, DNA precipitation using ethanol, estimation of DNA concentration and purity. Agarose gel electrophoresis of bacterial DNA, DNA visualisation and gel documentation. Preparation of PCR mixture for specific amplification of DNA of Salmonella and performance of PCR. Detection of PCR product using agarose gel electrophoresis and estimation of the length of PCR product. Estimation of PCR sensitivity. PCR with crude cell lysate after immunomagnetic separation (IMS) of cells Salmonella. This practical course is supplemented by course Bi6721.
At the end of this course, students should be able to practically carried out the basic polymerase chain reaction.

Syllabus

• 1. Safety of work in microbiology laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria.
• 2. Preparation of Salmonella Typhimurium LB5000 cells for isolation of bacterial DNA. Cell lysis.
• 3. DNA deproteination using phenol extraction. Precipitation of DNA with ethanol.
• 4. Estimation of DNA integrity using agarose gel electrophoresis of isolated DNA. DNA visualisation and gel documentation.
• 5. Estimation of DNA concentration and purity. Preparation of DNA in concentration suitable for PCR.
• 6. The work flow in PCR laboratory. Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. PCR reaction.
• 7. Detection of PCR product using agarose gel electrophoresis.
• 8. Estimation of amplicon length using known standards.
• 9. Preparation of PCR mixture from trude cell lysates. Positive and negative controls. PCR and detection of PCR produkt.
• 10.Imunomagnetic separation (IMS) of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR) with cells Salmonella. Estimation of PCR sensitivity.
• 11.I PCR products detection using agarose gel electropjoresis.
• 12. and 13. Identification of Salmonella cells in unknown sample using PCR.
• 14. Evaluation of protocols.Test.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Assessment methods

Training is enclosed by test.

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Timetable

Thu 9:00–11:50 Bpb,02012

Prerequisites (in Czech)

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )

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 12 student(s).
Current registration and enrolment status: enrolled: 0/12, only registered: 0/12, only registered with preference (fields directly associated with the programme): 0/12

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

I. Princips of work with DNA on model of plasmid DNA. Cultivation of bacterial cells E.coli JM109(pUC19). Microisolation of plasmid DNA pUC19. Preparation of agarose gel, gel electrophoresis of DNA, visualisation of DNA on gel, documentation. Purification of DNA. Elimination of RNA using LiCl and RNase A, proteins elimination using phenol extraction, precipitation of DNA by ethanol. Linearisation of plasmid DNA with restrictase EcoRI and estimation of restriction fragment lenght using program Anagel. II. PCR Salmonella. Isolation and purification of bacterial DNA Salmonella typhimurium LB5000 and Escherichia coli JM109. Spectrophotometric estimation of DNA concentration and purity.Preparation of PCR mixture for specific amplification of gene of Salmonella. Carry out of PCR and detection of PCR product. PCR with crude cell lysate. Immunomagnetic separation (IMS)of cells Salmonella from milk. IMS-cultivation of Salmonella cells. IMS-PCR of Salmonella cells.

Syllabus

• 1. Safety of work in microbiological and molecular biotechnological laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria. 2. Cultivation of bacterial cells E.coli JM109 and E. coli JM109(pUC19). Estimation of the presence of plasmids using cultivation of cells on plates with antibiotic. 3. Microisolation of plasmid DNA. 4. Preparation of 1% agarose gel. Gel electrophoresis of DNA. Visualisation of DNA and gel documentation. 5. Purification of DNA. Removing of RNA using LiCl and RNase A.Removing of proteins using phenol extraction. 6. Precipitation of DNA with ethanol.Checking of RNA removing and estimation of small concentrations of DNA using gel electrophoresis with standards containing known amount of DNA. 7. Linearisation of plasmid DNA with restrction nuclease EcoRI. Gel electrophoresis of cleaved DNA with DNA standards of known length. 8. Estimation of length of restriction fragment of DNA. The use of program Anagel. 9. Preparation of Salmonella typhimurium LB5000 and Escherichia coli JM109 cells for isolation of chromosomal DNA. Deproteination of DNA using phenol extraction. Precipitation of DNA using ethanol. 10.Spectrophotometric estimation of concentration and purity of DNA. The estimation of DNA integrity using agarose gel electrophoresis. 11.Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. Negative control.PCR reaction. 12.Detection of PCR product using agarose gel electrophoresis. The characterisation of PCR laboratory. 13.Preparation of crude cell lysate for PCR.Preparation of PCR mixture using crude cell lysate as DNA matrix. Pozitive and negative controls. Provodení PCR a detekce PCR produktu. 14.Imunomagnetic separation (IMS)of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR)with cells Salmonella. 15.Identifikation of Salmonella cells in unknown sample using PCR.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Assessment methods (in Czech)

Cvičení je ukončeno zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Timetable

Thu 9:00–11:50 Bpb,02012

Prerequisites (in Czech)

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )

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 12 student(s).
Current registration and enrolment status: enrolled: 0/12, only registered: 0/12, only registered with preference (fields directly associated with the programme): 0/12

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

I. Princips of work with DNA on model of plasmid DNA. Cultivation of bacterial cells E.coli JM109(pUC19). Microisolation of plasmid DNA pUC19. Preparation of agarose gel, gel electrophoresis of DNA, visualisation of DNA on gel, documentation. Purification of DNA. Elimination of RNA using LiCl and RNase A, proteins elimination using phenol extraction, precipitation of DNA by ethanol. Linearisation of plasmid DNA with restrictase EcoRI and estimation of restriction fragment lenght using program Anagel. II. PCR Salmonella. Isolation and purification of bacterial DNA Salmonella typhimurium LB5000 and Escherichia coli JM109. Spectrophotometric estimation of DNA concentration and purity.Preparation of PCR mixture for specific amplification of gene of Salmonella. Carry out of PCR and detection of PCR product. PCR with crude cell lysate. Immunomagnetic separation (IMS)of cells Salmonella from milk. IMS-cultivation of Salmonella cells. IMS-PCR of Salmonella cells.

Syllabus

• 1. Safety of work in microbiological and molecular biotechnological laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria. 2. Cultivation of bacterial cells E.coli JM109 and E. coli JM109(pUC19). Estimation of the presence of plasmids using cultivation of cells on plates with antibiotic. 3. Microisolation of plasmid DNA. 4. Preparation of 1% agarose gel. Gel electrophoresis of DNA. Visualisation of DNA and gel documentation. 5. Purification of DNA. Removing of RNA using LiCl and RNase A.Removing of proteins using phenol extraction. 6. Precipitation of DNA with ethanol.Checking of RNA removing and estimation of small concentrations of DNA using gel electrophoresis with standards containing known amount of DNA. 7. Linearisation of plasmid DNA with restrction nuclease EcoRI. Gel electrophoresis of cleaved DNA with DNA standards of known length. 8. Estimation of length of restriction fragment of DNA. The use of program Anagel. 9. Preparation of Salmonella typhimurium LB5000 and Escherichia coli JM109 cells for isolation of chromosomal DNA. Deproteination of DNA using phenol extraction. Precipitation of DNA using ethanol. 10.Spectrophotometric estimation of concentration and purity of DNA. The estimation of DNA integrity using agarose gel electrophoresis. 11.Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. Negative control.PCR reaction. 12.Detection of PCR product using agarose gel electrophoresis. The characterisation of PCR laboratory. 13.Preparation of crude cell lysate for PCR.Preparation of PCR mixture using crude cell lysate as DNA matrix. Pozitive and negative controls. Provodení PCR a detekce PCR produktu. 14.Imunomagnetic separation (IMS)of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR)with cells Salmonella. 15.Identifikation of Salmonella cells in unknown sample using PCR.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Assessment methods (in Czech)

Cvičení je ukončeno zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Ing. Bohuslav Rittich, CSc. (lecturer)
doc. RNDr. Alena Španová, CSc. (lecturer)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
doc. RNDr. Alena Španová, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Timetable of Seminar Groups

Bi6721c/01: Thu 8:00–10:50 Bpb,02012
Bi6721c/02: Thu 11:00–13:50 Bpb,02012

Prerequisites (in Czech)

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )

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 12 student(s).
Current registration and enrolment status: enrolled: 0/12, only registered: 0/12, only registered with preference (fields directly associated with the programme): 0/12

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

I. Princips of work with DNA on model of plasmid DNA. Cultivation of bacterial cells E.coli JM109(pUC19). Microisolation of plasmid DNA pUC19. Preparation of agarose gel, gel electrophoresis of DNA, visualisation of DNA on gel, documentation. Purification of DNA. Elimination of RNA using LiCl and RNase A, proteins elimination using phenol extraction, precipitation of DNA by ethanol. Linearisation of plasmid DNA with restrictase EcoRI and estimation of restriction fragment lenght using program Anagel. II. PCR Salmonella. Isolation and purification of bacterial DNA Salmonella typhimurium LB5000 and Escherichia coli JM109. Spectrophotometric estimation of DNA concentration and purity.Preparation of PCR mixture for specific amplification of gene of Salmonella. Carry out of PCR and detection of PCR product. PCR with crude cell lysate. Immunomagnetic separation (IMS)of cells Salmonella from milk. IMS-cultivation of Salmonella cells. IMS-PCR of Salmonella cells.

Syllabus

• 1. Safety of work in microbiological and molecular biotechnological laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria. 2. Cultivation of bacterial cells E.coli JM109 and E. coli JM109(pUC19). Estimation of the presence of plasmids using cultivation of cells on plates with antibiotic. 3. Microisolation of plasmid DNA. 4. Preparation of 1% agarose gel. Gel electrophoresis of DNA. Visualisation of DNA and gel documentation. 5. Purification of DNA. Removing of RNA using LiCl and RNase A.Removing of proteins using phenol extraction. 6. Precipitation of DNA with ethanol.Checking of RNA removing and estimation of small concentrations of DNA using gel electrophoresis with standards containing known amount of DNA. 7. Linearisation of plasmid DNA with restrction nuclease EcoRI. Gel electrophoresis of cleaved DNA with DNA standards of known length. 8. Estimation of length of restriction fragment of DNA. The use of program Anagel. 9. Preparation of Salmonella typhimurium LB5000 and Escherichia coli JM109 cells for isolation of chromosomal DNA. Deproteination of DNA using phenol extraction. Precipitation of DNA using ethanol. 10.Spectrophotometric estimation of concentration and purity of DNA. The estimation of DNA integrity using agarose gel electrophoresis. 11.Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. Negative control.PCR reaction. 12.Detection of PCR product using agarose gel electrophoresis. The characterisation of PCR laboratory. 13.Preparation of crude cell lysate for PCR.Preparation of PCR mixture using crude cell lysate as DNA matrix. Pozitive and negative controls. Provodení PCR a detekce PCR produktu. 14.Imunomagnetic separation (IMS)of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR)with cells Salmonella. 15.Identifikation of Salmonella cells in unknown sample using PCR.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Assessment methods (in Czech)

Cvičení je ukončeno zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Ing. Bohuslav Rittich, CSc. (lecturer)
doc. RNDr. Alena Španová, CSc. (lecturer)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
doc. RNDr. Alena Španová, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Timetable of Seminar Groups

Bi6721c/01: Thu 11:00–13:50 Bpb,02012, A. Španová
Bi6721c/02: Thu 8:00–10:50 Bpb,02012, A. Španová

Prerequisites (in Czech)

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )

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 12 student(s).
Current registration and enrolment status: enrolled: 0/12, only registered: 0/12, only registered with preference (fields directly associated with the programme): 0/12

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

I. Princips of work with DNA on model of plasmid DNA. Cultivation of bacterial cells E.coli JM109(pUC19). Microisolation of plasmid DNA pUC19. Preparation of agarose gel, gel electrophoresis of DNA, visualisation of DNA on gel, documentation. Purification of DNA. Elimination of RNA using LiCl and RNase A, proteins elimination using phenol extraction, precipitation of DNA by ethanol. Linearisation of plasmid DNA with restrictase EcoRI and estimation of restriction fragment lenght using program Anagel. II. PCR Salmonella. Isolation and purification of bacterial DNA Salmonella typhimurium LB5000 and Escherichia coli JM109. Spectrophotometric estimation of DNA concentration and purity.Preparation of PCR mixture for specific amplification of gene of Salmonella. Carry out of PCR and detection of PCR product. PCR with crude cell lysate. Immunomagnetic separation (IMS)of cells Salmonella from milk. IMS-cultivation of Salmonella cells. IMS-PCR of Salmonella cells.

Syllabus

• 1. Safety of work in microbiological and molecular biotechnological laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria. 2. Cultivation of bacterial cells E.coli JM109 and E. coli JM109(pUC19). Estimation of the presence of plasmids using cultivation of cells on plates with antibiotic. 3. Microisolation of plasmid DNA. 4. Preparation of 1% agarose gel. Gel electrophoresis of DNA. Visualisation of DNA and gel documentation. 5. Purification of DNA. Removing of RNA using LiCl and RNase A.Removing of proteins using phenol extraction. 6. Precipitation of DNA with ethanol.Checking of RNA removing and estimation of small concentrations of DNA using gel electrophoresis with standards containing known amount of DNA. 7. Linearisation of plasmid DNA with restrction nuclease EcoRI. Gel electrophoresis of cleaved DNA with DNA standards of known length. 8. Estimation of length of restriction fragment of DNA. The use of program Anagel. 9. Preparation of Salmonella typhimurium LB5000 and Escherichia coli JM109 cells for isolation of chromosomal DNA. Deproteination of DNA using phenol extraction. Precipitation of DNA using ethanol. 10.Spectrophotometric estimation of concentration and purity of DNA. The estimation of DNA integrity using agarose gel electrophoresis. 11.Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. Negative control.PCR reaction. 12.Detection of PCR product using agarose gel electrophoresis. The characterisation of PCR laboratory. 13.Preparation of crude cell lysate for PCR.Preparation of PCR mixture using crude cell lysate as DNA matrix. Pozitive and negative controls. Provodení PCR a detekce PCR produktu. 14.Imunomagnetic separation (IMS)of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR)with cells Salmonella. 15.Identifikation of Salmonella cells in unknown sample using PCR.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Assessment methods (in Czech)

Cvičení je ukončeno zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Ing. Bohuslav Rittich, CSc. (lecturer)
doc. RNDr. Alena Španová, CSc. (lecturer)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
doc. RNDr. Alena Španová, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Prerequisites (in Czech)

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )

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 12 student(s).
Current registration and enrolment status: enrolled: 0/12, only registered: 0/12, only registered with preference (fields directly associated with the programme): 0/12

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

I. Princips of work with DNA on model of plasmid DNA. Cultivation of bacterial cells E.coli JM109(pUC19). Microisolation of plasmid DNA pUC19. Preparation of agarose gel, gel electrophoresis of DNA, visualisation of DNA on gel, documentation. Purification of DNA. Elimination of RNA using LiCl and RNase A, proteins elimination using phenol extraction, precipitation of DNA by ethanol. Linearisation of plasmid DNA with restrictase EcoRI and estimation of restriction fragment lenght using program Anagel. II. PCR Salmonella. Isolation and purification of bacterial DNA Salmonella typhimurium LB5000 and Escherichia coli JM109. Spectrophotometric estimation of DNA concentration and purity.Preparation of PCR mixture for specific amplification of gene of Salmonella. Carry out of PCR and detection of PCR product. PCR with crude cell lysate. Immunomagnetic separation (IMS)of cells Salmonella from milk. IMS-cultivation of Salmonella cells. IMS-PCR of Salmonella cells.

Syllabus

• 1. Safety of work in microbiological and molecular biotechnological laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria. 2. Cultivation of bacterial cells E.coli JM109 and E. coli JM109(pUC19). Estimation of the presence of plasmids using cultivation of cells on plates with antibiotic. 3. Microisolation of plasmid DNA. 4. Preparation of 1% agarose gel. Gel electrophoresis of DNA. Visualisation of DNA and gel documentation. 5. Purification of DNA. Removing of RNA using LiCl and RNase A.Removing of proteins using phenol extraction. 6. Precipitation of DNA with ethanol.Checking of RNA removing and estimation of small concentrations of DNA using gel electrophoresis with standards containing known amount of DNA. 7. Linearisation of plasmid DNA with restrction nuclease EcoRI. Gel electrophoresis of cleaved DNA with DNA standards of known length. 8. Estimation of length of restriction fragment of DNA. The use of program Anagel. 9. Preparation of Salmonella typhimurium LB5000 and Escherichia coli JM109 cells for isolation of chromosomal DNA. Deproteination of DNA using phenol extraction. Precipitation of DNA using ethanol. 10.Spectrophotometric estimation of concentration and purity of DNA. The estimation of DNA integrity using agarose gel electrophoresis. 11.Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. Negative control.PCR reaction. 12.Detection of PCR product using agarose gel electrophoresis. The characterisation of PCR laboratory. 13.Preparation of crude cell lysate for PCR.Preparation of PCR mixture using crude cell lysate as DNA matrix. Pozitive and negative controls. Provodení PCR a detekce PCR produktu. 14.Imunomagnetic separation (IMS)of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR)with cells Salmonella. 15.Identifikation of Salmonella cells in unknown sample using PCR.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Assessment methods (in Czech)

Cvičení je ukončeno zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: every week.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Ing. Bohuslav Rittich, CSc. (lecturer)
doc. RNDr. Alena Španová, CSc. (lecturer)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
doc. RNDr. Alena Španová, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

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 12 student(s).
Current registration and enrolment status: enrolled: 0/12, only registered: 0/12, only registered with preference (fields directly associated with the programme): 0/12

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

I. Princips of work with DNA on model of plasmid DNA. Cultivation of bacterial cells E.coli JM109(pUC19). Microisolation of plasmid DNA pUC19. Preparation of agarose gel, gel electrophoresis of DNA, visualisation of DNA on gel, documentation. Purification of DNA. Elimination of RNA using LiCl and RNase A, proteins elimination using phenol extraction, precipitation of DNA by ethanol. Linearisation of plasmid DNA with restrictase EcoRI and estimation of restriction fragment lenght using program Anagel. II. PCR Salmonella. Isolation and purification of bacterial DNA Salmonella typhimurium LB5000 and Escherichia coli JM109. Spectrophotometric estimation of DNA concentration and purity.Preparation of PCR mixture for specific amplification of gene of Salmonella. Carry out of PCR and detection of PCR product. PCR with crude cell lysate. Immunomagnetic separation (IMS)of cells Salmonella from milk. IMS-cultivation of Salmonella cells. IMS-PCR of Salmonella cells.

Syllabus

• 1. Safety of work in microbiological and molecular biotechnological laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria. 2. Cultivation of bacterial cells E.coli JM109 and E. coli JM109(pUC19). Estimation of the presence of plasmids using cultivation of cells on plates with antibiotic. 3. Microisolation of plasmid DNA. 4. Preparation of 1% agarose gel. Gel electrophoresis of DNA. Visualisation of DNA and gel documentation. 5. Purification of DNA. Removing of RNA using LiCl and RNase A.Removing of proteins using phenol extraction. 6. Precipitation of DNA with ethanol.Checking of RNA removing and estimation of small concentrations of DNA using gel electrophoresis with standards containing known amount of DNA. 7. Linearisation of plasmid DNA with restrction nuclease EcoRI. Gel electrophoresis of cleaved DNA with DNA standards of known length. 8. Estimation of length of restriction fragment of DNA. The use of program Anagel. 9. Preparation of Salmonella typhimurium LB5000 and Escherichia coli JM109 cells for isolation of chromosomal DNA. Deproteination of DNA using phenol extraction. Precipitation of DNA using ethanol. 10.Spectrophotometric estimation of concentration and purity of DNA. The estimation of DNA integrity using agarose gel electrophoresis. 11.Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. Negative control.PCR reaction. 12.Detection of PCR product using agarose gel electrophoresis. The characterisation of PCR laboratory. 13.Preparation of crude cell lysate for PCR.Preparation of PCR mixture using crude cell lysate as DNA matrix. Pozitive and negative controls. Provodení PCR a detekce PCR produktu. 14.Imunomagnetic separation (IMS)of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR)with cells Salmonella. 15.Identifikation of Salmonella cells in unknown sample using PCR.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Assessment methods (in Czech)

Cvičení je ukončeno zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further Comments

The course is taught annually.
The course is taught: every week.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

The course is not taught in Spring 2023

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. Mgr. Pavel Dvořák, Ph.D. (seminar tutor)
Mgr. Barbora Burýšková (seminar tutor)
Mgr. Barbora Popelářová (seminar tutor)
Mgr. Barbora Jankovičová (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: 0/10, 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 the practical course is to acquaint students with the method of isolation of plasmid and genomic DNA of bacteria using a kit, with the design of oligonucleotide primers and preparation of polymerase chain reaction (end-point and quantitative real-time PCR), with the method of control gel electrophoresis, sequence analysis, and with the purification of the foreign protein from the host bacterium by affinity chromatography.

Learning outcomes

At the end of this course, the students should be able to use practically the microbial DNA isolation protocol, the method of polymerase chain reaction, sequence analysis, and the gel electrophoresis method.

Syllabus

• 1. Preparation of bacterial lysates from cultures of Pseudomonas putida and Escherichia coli.
• 2. Amplification of four specific genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 9. Polymerase chain reaction by system end-point, gel electrophoresis.
• 10. Real-time PCR with DNA sample from cytomegalovirus.
• 11. Purification of a recombinant protein from Escherichia coli 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 practice takes place once in 14 days. Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v  the first practice and lecture). In the protocols students describe, compare, analyze, evaluated and discuss 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)

Study Materials
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.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

The course is not taught in Spring 2015

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Milan Bartoš, Ph.D. (seminar tutor)
Mgr. Jana Čmielová, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Zdeněk Hubálek, DrSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Milan Bartoš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Tue 13:00–15:50 E25/111

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

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 24 student(s).
Current registration and enrolment status: enrolled: 0/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

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

At the end of this course, the students should be able practically use the isolation of DNA, the method of polymerase chain reaction and gel electrophoresis from samples of bacterial and yeast cells.

Syllabus

• 1. Příprava bakteriálních lyzátů z kultur čeledi Pasteurellaceae.
• 2. Amplification of three genes.
• 3. Gel electrophoresis of the amplification, purification of the PCR products.
• 4. Electrophoresis of the purification PCR products, quantification and preparation of the sample for the sending and DNA sequencing.
• 5. In silico analysis of the DNA sequencing.
• 6. Isolation of the genomic DNA - bacterial culture Escherichia coli.
• 7. Estimation of the concentration and purity of the DNA spectrophotometrically.
• 8. Isolation of the genomic DNA from the sample with Chlamydia trachomatis.
• 9. Indicative estimation of the concentration and the purity of the DNA spectrofotometrically.
• 10. Polymerase chain reaction by system end-point, gel electrophoresis.
• 11. Real-time PCR - Chlamydia trachomatis.
• 12. Isolation DNA from yeasts (phenol-chloroform extraction), gel electrophoresis.
• 13. PCR of the ITS region for differentiation complex Saccharomyces sensu stricto, gelová electrophoresis.
• 14. Cleavage of the PCR products by restriction endonucleasis, gel electrophoresis.

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

Students work individually and process their own sample. The results of experiments have to be summarized and evaluated in protocols. The protocols are prepared in accordance (information v the first practise and lecture). In the protocols students describe, compare, analyze, evaluated and discuss own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

The course is not taught in Spring 2013

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

Bartoš (seminar tutor), prof. RNDr. Zdeněk Hubálek, DrSc. (deputy)
Mgr. Jana Čmielová, Ph.D. (seminar tutor)

Guaranteed by

prof. RNDr. Zdeněk Hubálek, DrSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• Special Biology (programme PřF, B-EXB)
• Special Biology (programme PřF, B-EXB, specialization Mikrobiology a Molecular Biotechnology)
• Special Biology (programme PřF, N-EXB)
• Special Biology (programme PřF, N-EXB, specialization Mikrobiologie a molekulární biotechnologie)

Course objectives

At the end of this course, the students should be able practically use the method of polymerase chain reaction for the identification of bacteria.

Syllabus

• 1. Safety of work in microbiology laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria.
• 2. Preparation of Salmonella Typhimurium LB5000 cells for isolation of bacterial DNA. Cell lysis.
• 3. DNA deproteination using phenol extraction. Precipitation of DNA with ethanol.
• 4. Estimation of DNA integrity using agarose gel electrophoresis of isolated DNA. DNA visualisation and gel documentation.
• 5. Estimation of DNA concentration and purity. Preparation of DNA in concentration suitable for PCR.
• 6. The work flow in PCR laboratory. Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. PCR reaction.
• 7. Detection of PCR product using agarose gel electrophoresis.
• 8. Estimation of amplicon length using known standards.
• 9. Preparation of PCR mixture from trude cell lysates. Positive and negative controls. PCR and detection of PCR produkt.
• 10.Imunomagnetic separation (IMS) of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR) with cells Salmonella. Estimation of PCR sensitivity.
• 11.I PCR products detection using agarose gel electropjoresis.
• 12. and 13. Identification of Salmonella cells in unknown sample using PCR.
• 14. Evaluation of protocols.Test.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Teaching methods

Each student works independently and processes his or her own sample during the laboratory course. The results of their experiments must be evaluated in a protocol. The protocols (4 in number) are elaborated in the form of a poster according to the following scheme: Introduction, Aim of work, Material and methods, Results, Discussion, Conclusion. In the protocol each student describes, compares, analyses, evaluates, and discusses his or her own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols (4). In the course of the credit exercise, each student has to identify target bacteria in an unknown sample using the PCR method.

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: every week.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I - practical course

The course is not taught in Spring 2012

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

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

At the end of this course, the students should be able practically use the method of polymerase chain reaction for the identification of bacteria.

Syllabus

• 1. Safety of work in microbiology laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria.
• 2. Preparation of Salmonella Typhimurium LB5000 cells for isolation of bacterial DNA. Cell lysis.
• 3. DNA deproteination using phenol extraction. Precipitation of DNA with ethanol.
• 4. Estimation of DNA integrity using agarose gel electrophoresis of isolated DNA. DNA visualisation and gel documentation.
• 5. Estimation of DNA concentration and purity. Preparation of DNA in concentration suitable for PCR.
• 6. The work flow in PCR laboratory. Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. PCR reaction.
• 7. Detection of PCR product using agarose gel electrophoresis.
• 8. Estimation of amplicon length using known standards.
• 9. Preparation of PCR mixture from trude cell lysates. Positive and negative controls. PCR and detection of PCR produkt.
• 10.Imunomagnetic separation (IMS) of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR) with cells Salmonella. Estimation of PCR sensitivity.
• 11.I PCR products detection using agarose gel electropjoresis.
• 12. and 13. Identification of Salmonella cells in unknown sample using PCR.
• 14. Evaluation of protocols.Test.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Teaching methods

Each student works independently and processes his or her own sample during the laboratory course. The results of their experiments must be evaluated in a protocol. The protocols (4 in number) are elaborated in the form of a poster according to the following scheme: Introduction, Aim of work, Material and methods, Results, Discussion, Conclusion. In the protocol each student describes, compares, analyses, evaluates, and discusses his or her own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols (4). In the course of the credit exercise, each student has to identify target bacteria in an unknown sample using the PCR method.

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.
The course is taught: every week.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

The information about the term spring 2012 - acreditation is not made public

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

At the end of this course, the students should be able practically use the method of polymerase chain reaction for the identification of bacteria.

Syllabus

• 1. Safety of work in microbiology laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria.
• 2. Preparation of Salmonella Typhimurium LB5000 cells for isolation of bacterial DNA. Cell lysis.
• 3. DNA deproteination using phenol extraction. Precipitation of DNA with ethanol.
• 4. Estimation of DNA integrity using agarose gel electrophoresis of isolated DNA. DNA visualisation and gel documentation.
• 5. Estimation of DNA concentration and purity. Preparation of DNA in concentration suitable for PCR.
• 6. The work flow in PCR laboratory. Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. PCR reaction.
• 7. Detection of PCR product using agarose gel electrophoresis.
• 8. Estimation of amplicon length using known standards.
• 9. Preparation of PCR mixture from trude cell lysates. Positive and negative controls. PCR and detection of PCR produkt.
• 10.Imunomagnetic separation (IMS) of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR) with cells Salmonella. Estimation of PCR sensitivity.
• 11.I PCR products detection using agarose gel electropjoresis.
• 12. and 13. Identification of Salmonella cells in unknown sample using PCR.
• 14. Evaluation of protocols.Test.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Teaching methods

Each student works independently and processes his or her own sample during the laboratory course. The results of their experiments must be evaluated in a protocol. The protocols (4 in number) are elaborated in the form of a poster according to the following scheme: Introduction, Aim of work, Material and methods, Results, Discussion, Conclusion. In the protocol each student describes, compares, analyses, evaluates, and discusses his or her own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols (4). In the course of the credit exercise, each student has to identify target bacteria in an unknown sample using the PCR method.

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: every week.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Prerequisites

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )
The course is destined for students interested in practical knowledge of method PCR (polymerase chain reaction).

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

At the end of this course, the students should be able practically use the method of polymerase chain reaction for the identification of bacteria.

Syllabus

• 1. Safety of work in microbiology laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria.
• 2. Preparation of Salmonella Typhimurium LB5000 cells for isolation of bacterial DNA. Cell lysis.
• 3. DNA deproteination using phenol extraction. Precipitation of DNA with ethanol.
• 4. Estimation of DNA integrity using agarose gel electrophoresis of isolated DNA. DNA visualisation and gel documentation.
• 5. Estimation of DNA concentration and purity. Preparation of DNA in concentration suitable for PCR.
• 6. The work flow in PCR laboratory. Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. PCR reaction.
• 7. Detection of PCR product using agarose gel electrophoresis.
• 8. Estimation of amplicon length using known standards.
• 9. Preparation of PCR mixture from trude cell lysates. Positive and negative controls. PCR and detection of PCR produkt.
• 10.Imunomagnetic separation (IMS) of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR) with cells Salmonella. Estimation of PCR sensitivity.
• 11.I PCR products detection using agarose gel electropjoresis.
• 12. and 13. Identification of Salmonella cells in unknown sample using PCR.
• 14. Evaluation of protocols.Test.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Teaching methods

Each student works independently and processes his or her own sample during the laboratory course. The results of their experiments must be evaluated in a protocol. The protocols (4 in number) are elaborated in the form of a poster according to the following scheme: Introduction, Aim of work, Material and methods, Results, Discussion, Conclusion. In the protocol each student describes, compares, analyses, evaluates, and discusses his or her own results.

Assessment methods

The course is closed by a course-unit credit. The students obtain their credits for active attendance at the course and for the preparation of protocols (4). In the course of the credit exercise, each student has to identify target bacteria in an unknown sample using the PCR method.

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: every week.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

Bi6721c Special Methods of Microorganisms Analysis I. - practical course

Extent and Intensity

0/3/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

doc. RNDr. Alena Španová, CSc. (seminar tutor)
doc. Ing. Bohuslav Rittich, CSc. (seminar tutor)
RNDr. Aleš Kovařík, CSc. (seminar tutor)

Guaranteed by

doc. Ing. Bohuslav Rittich, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Ing. Bohuslav Rittich, CSc.

Prerequisites (in Czech)

NOW( Bi6721 Spec. Meth. Microorg. Anal. I. )

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 12 student(s).
Current registration and enrolment status: enrolled: 0/12, only registered: 0/12, only registered with preference (fields directly associated with the programme): 0/12

fields of study / plans the course is directly associated with

• General Biology (programme PřF, B-BI, specialization Microbiology)
• General Biology (programme PřF, M-BI, specialization Microbiology)
• General Biology (programme PřF, N-BI, specialization Microbiology)

Course objectives

I. Princips of work with DNA on model of plasmid DNA. Cultivation of bacterial cells E.coli JM109(pUC19). Microisolation of plasmid DNA pUC19. Preparation of agarose gel, gel electrophoresis of DNA, visualisation of DNA on gel, documentation. Purification of DNA. Elimination of RNA using LiCl and RNase A, proteins elimination using phenol extraction, precipitation of DNA by ethanol. Linearisation of plasmid DNA with restrictase EcoRI and estimation of restriction fragment lenght using program Anagel. II. PCR Salmonella. Isolation and purification of bacterial DNA Salmonella typhimurium LB5000 and Escherichia coli JM109. Spectrophotometric estimation of DNA concentration and purity.Preparation of PCR mixture for specific amplification of gene of Salmonella. Carry out of PCR and detection of PCR product. PCR with crude cell lysate. Immunomagnetic separation (IMS)of cells Salmonella from milk. IMS-cultivation of Salmonella cells. IMS-PCR of Salmonella cells.

Syllabus

• 1. Safety of work in microbiological and molecular biotechnological laboratory. Pipeting of small volumes of solvents using pippetmans. Preparation of media for cultivation of bacteria. 2. Cultivation of bacterial cells E.coli JM109 and E. coli JM109(pUC19). Estimation of the presence of plasmids using cultivation of cells on plates with antibiotic. 3. Microisolation of plasmid DNA. 4. Preparation of 1% agarose gel. Gel electrophoresis of DNA. Visualisation of DNA and gel documentation. 5. Purification of DNA. Removing of RNA using LiCl and RNase A.Removing of proteins using phenol extraction. 6. Precipitation of DNA with ethanol.Checking of RNA removing and estimation of small concentrations of DNA using gel electrophoresis with standards containing known amount of DNA. 7. Linearisation of plasmid DNA with restrction nuclease EcoRI. Gel electrophoresis of cleaved DNA with DNA standards of known length. 8. Estimation of length of restriction fragment of DNA. The use of program Anagel. 9. Preparation of Salmonella typhimurium LB5000 and Escherichia coli JM109 cells for isolation of chromosomal DNA. Deproteination of DNA using phenol extraction. Precipitation of DNA using ethanol. 10.Spectrophotometric estimation of concentration and purity of DNA. The estimation of DNA integrity using agarose gel electrophoresis. 11.Preparation of PCR mixture for specific amplification of gene Salmonella using purified DNA as DNA matrix. Negative control.PCR reaction. 12.Detection of PCR product using agarose gel electrophoresis. The characterisation of PCR laboratory. 13.Preparation of crude cell lysate for PCR.Preparation of PCR mixture using crude cell lysate as DNA matrix. Pozitive and negative controls. Provodení PCR a detekce PCR produktu. 14.Imunomagnetic separation (IMS)of cells Salmonella. IMS-cultivation (IMS-CM) of cells Salmonella. IMS-polymerase chain reaction (IMS-PCR)with cells Salmonella. 15.Identifikation of Salmonella cells in unknown sample using PCR.

Literature

• F.Sambrook and D.W. Russell Molecular Cloning. A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press. 2001

Assessment methods (in Czech)

Cvičení je ukončeno zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7430 Molecular biotechnology
• Bi7722 Methods of Microorganisms Analysis II

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: every week.
Information on course enrolment limitations: Přednost mají posluchači specializace mikrobiologie.

• Enrolment Statistics (recent)