Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2019
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Mgr. Jarmila Navrátilová, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 18. 2. to Fri 17. 5. Thu 7:00–12:50 D36/216, Fri 9:00–14:50 D36/216
  • Timetable of Seminar Groups:
Bi6405/11_duben: No timetable has been entered into IS.
Bi6405/2_kveten: No timetable has been entered into IS.
Bi6405/25_duben: No timetable has been entered into IS.
Bi6405/28_brezen: No timetable has been entered into IS.
Bi6405/4_duben: No timetable has been entered into IS.
Bi6405/9_kveten: No timetable has been entered into IS.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
spring 2018
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Mgr. Jarmila Navrátilová, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Thu 7:00–12:50 D36/216, Fri 9:00–14:50 D36/216
  • Timetable of Seminar Groups:
Bi6405/01: No timetable has been entered into IS.
Bi6405/02: No timetable has been entered into IS.
Bi6405/03: No timetable has been entered into IS.
Bi6405/04: No timetable has been entered into IS.
Bi6405/05: No timetable has been entered into IS.
Bi6405/06: No timetable has been entered into IS.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2017
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 20. 2. to Mon 22. 5. Thu 7:00–12:50 D36/216, Fri 9:00–14:50 D36/216
  • Timetable of Seminar Groups:
Bi6405/04_05_2017: No timetable has been entered into IS.
Bi6405/06_04_2017: No timetable has been entered into IS.
Bi6405/11_05_2017: No timetable has been entered into IS.
Bi6405/20_04_2017: No timetable has been entered into IS.
Bi6405/27_04_2017: No timetable has been entered into IS.
Bi6405/30_03_2017: No timetable has been entered into IS.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2016
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Thu 7:00–12:50 D36/216, Fri 9:00–14:50 D36/216
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligases; to perform separation of DNA and protein molecules by gel electrophoresis; to elute DNA molecules out of a agarose gels, to perform immunoblotting and to learn ways of successful transfection of plasmid DNA into eukaryotic cells. At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5´ overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis). 10. Recombinant plasmid transfection into mammlian cells. 11. Cell lysis, protein electrophoresis and immunoblotting.
Literature
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Brief lecture follwed by practical laboratory training, class discussion.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2015
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Mgr. Jarmila Navrátilová, Ph.D. (seminar tutor)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Thu 7:00–12:50 D36/216, Fri 9:00–14:50 D36/216
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligases; to perform separation of DNA and protein molecules by gel electrophoresis; to elute DNA molecules out of a agarose gels, to perform immunoblotting and to learn ways of successful transfection of plasmid DNA into eukaryotic cells. At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5´ overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis). 10. Recombinant plasmid transfection into mammlian cells. 11. Cell lysis, protein electrophoresis and immunoblotting.
Literature
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Brief lecture follwed by practical laboratory training, class discussion.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2014
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Thu 7:00–12:50 D36/216, Fri 9:00–14:50 D36/216
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligases; to perform separation of DNA and protein molecules by gel electrophoresis; to elute DNA molecules out of a agarose gels, to perform immunoblotting and to learn ways of successful transfection of plasmid DNA into eukaryotic cells. At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5´ overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis). 10. Recombinant plasmid transfection into mammlian cells. 11. Cell lysis, protein electrophoresis and immunoblotting.
Literature
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Brief lecture follwed by practical laboratory training, class discussion.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2013
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Thu 11:00–16:50 C03/228, Fri 9:00–14:50 C03/228
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligases; to perform separation of DNA and protein molecules by gel electrophoresis; to elute DNA molecules out of a agarose gels, to perform immunoblotting and to learn ways of successful transfection of plasmid DNA into eukaryotic cells. At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5´ overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis). 10. Recombinant plasmid transfection into mammlian cells. 11. Cell lysis, protein electrophoresis and immunoblotting.
Literature
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Brief lecture follwed by practical laboratory training, class discussion.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2012
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Thu 11:00–16:50 C03/LCD, Fri 9:00–14:50 C03/LCD
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligaes; to perform separation of DNA molecules by agarose gel electrophoresis to elute DNA molecules out of a agarose gels At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Teaching methods
Brief lecture follwed by practical laboratory training.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2011
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Timetable of Seminar Groups
Bi6405/01: Thu 8:00–13:50 C03/LCD, P. Beneš
Bi6405/02: Wed 8:00–13:50 C03/LCD, P. Beneš
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligaes; to perform separation of DNA molecules by agarose gel electrophoresis to elute DNA molecules out of a agarose gels At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Teaching methods
Brief lecture follwed by practical laboratory training.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2010
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Timetable of Seminar Groups
Bi6405/01: Tue 9:00–14:50 Kontaktujte učitele, P. Beneš, Nepřihlašuje se, výuka poběží blokově v uvedených termínech.
Bi6405/02: Mon 11:00–16:50 Kontaktujte učitele, P. Beneš, Nepřihlašuje se, výuka poběží blokově v uvedených termínech.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligaes; to perform separation of DNA molecules by agarose gel electrophoresis to elute DNA molecules out of a agarose gels At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Teaching methods
Brief lecture follwed by practical laboratory training.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2009
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligaes; to perform separation of DNA molecules by agarose gel electrophoresis to elute DNA molecules out of a agarose gels
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2008
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Timetable of Seminar Groups
Bi6405/0730: No timetable has been entered into IS. P. Beneš
Bi6405/1130: No timetable has been entered into IS. P. Beneš
Bi6405/1530: No timetable has been entered into IS. P. Beneš
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skils from microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course acquire experience with DNA molecule manipulations in vitro to obtain recombinant DNA molecules. The aim of the course is to teach the ways of successful purification of pure plasmid DNA from bacterial cells, its fragmentation using various restriction enzymes, modifications of DNA termini and ligation with other DNA molecules. In addition, students get experience with DNA electrophoresis and gel elution.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Assessment methods (in Czech)
zápočet se udílí za aktivní přístup, účast ve výuce a vypacování kvalitních protokolů z jednotlivých úloh.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2007
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skils from microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course acquire experience with DNA molecule manipulations in vitro to obtain recombinant DNA molecules. The aim of the course is to teach the ways of successful purification of pure plasmid DNA from bacterial cells, its fragmentation using various restriction enzymes, modifications of DNA termini and ligation with other DNA molecules. In addition, students get experience with DNA electrophoresis and gel elution.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Assessment methods (in Czech)
zápočet se udílí za aktivní přístup, účast ve výuce a vypacování kvalitních protokolů z jednotlivých úloh.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2006
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skils from microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course acquire experience with DNA molecule manipulations in vitro to obtain recombinant DNA molecules. The aim of the course is to teach the ways of successful purification of pure plasmid DNA from bacterial cells, its fragmentation using various restriction enzymes, modifications of DNA termini and ligation with other DNA molecules. In addition, students get experience with DNA electrophoresis and gel elution.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Assessment methods (in Czech)
zápočet se udílí za aktivní přístup, účast ve výuce a vypacování kvalitních protokolů z jednotlivých úloh.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2005
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Timetable
Tue 7:00–12:50 Bpr,02004
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skils from microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course acquire experience with DNA molecule manipulations in vitro to obtain recombinant DNA molecules. The aim of the course is to teach the ways of successful purification of pure plasmid DNA from bacterial cells, its fragmentation using various restriction enzymes, modifications of DNA termini and ligation with other DNA molecules. In addition, students get experience with DNA electrophoresis and gel elution.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Assessment methods (in Czech)
zápočet se udílí za aktivní přístup, účast ve výuce a vypacování kvalitních protokolů z jednotlivých úloh.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2004
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skils from microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course acquire experience with DNA molecule manipulations in vitro to obtain recombinant DNA molecules. The aim of the course is to teach the ways of successful purification of pure plasmid DNA from bacterial cells, its fragmentation using various restriction enzymes, modifications of DNA termini and ligation with other DNA molecules. In addition, students get experience with DNA electrophoresis and gel elution.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Assessment methods (in Czech)
zápočet se udílí za aktivní přístup, účast ve výuce a vypacování kvalitních protokolů z jednotlivých úloh.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2003
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Timetable of Seminar Groups
Bi6405/01: No timetable has been entered into IS.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skils from microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course acquire experience with DNA molecule manipulations in vitro to obtain recombinant DNA molecules. The aim of the course is to teach the ways of successful purification of pure plasmid DNA from bacterial cells, its fragmentation using various restriction enzymes, modifications of DNA termini and ligation with other DNA molecules. In addition, students get experience with DNA electrophoresis and gel elution.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Assessment methods (in Czech)
zápočet se udílí za aktivní přístup, účast ve výuce a vypacování kvalitních protokolů z jednotlivých úloh.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2025

The course is not taught in Spring 2025

Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Guaranteed by
prof. Mgr. Petr Beneš, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2024

The course is not taught in Spring 2024

Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Guaranteed by
prof. Mgr. Petr Beneš, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2023

The course is not taught in Spring 2023

Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Guaranteed by
prof. Mgr. Petr Beneš, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2022

The course is not taught in Spring 2022

Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Guaranteed by
prof. Mgr. Petr Beneš, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2021

The course is not taught in Spring 2021

Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Guaranteed by
prof. Mgr. Petr Beneš, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2020

The course is not taught in Spring 2020

Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Guaranteed by
prof. Mgr. Petr Beneš, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Petr Beneš, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic computer competency, fundamental knowledge of molecular biology and bioinformatics and practical skills in microbiology, biochemistry and molecular biology as, for example, manipulation with automatic pipettes, preparation of buffers and cultivation media, sterile liquide and bacterial cultures handling, centrifugation, and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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
The aim of this course is to prepare and realize a project for silencing target gene expression using CRISPR/Cas9 a shRNA methodology.
Learning outcomes
At the end of this course, students will be able to to identify CRISPR/Cas9 and siRNA targets in sequence of gene of interest using public bioinformatic tools, to create and purify recombinant CRISPR/Cas9 and shRNA vectors, to transfect these vectors into mammalian cells, to analyze mutational status of target gene and to evaluate gene expression. Students will be ale to use the acquired knowledge to prepare and to implement a project analyzing the function of selected genes in diverse biological processes.
Syllabus
  • 1. Introductory lecture – gene edditing, CRISPR/Cas9, RNA interference, bioinformatic tools – gene sequence search, sequence alignment, design of CRISPR/Cas9 and shRNA targets, open reading frame finder. 2. Preparation of individual written protocols by students with the aim to design CRISPR/Cas9 and shRNA vectors for target gene. 3. Evaluation of protocols by a teacher. 4. Implementation of experimental protocol in the lab – preparation and purification of recombinant CRISPR/Cas9 and shRNA vectors, mammalian cells transfection, cells harvestion and lysis, determination of protein concentration, SDS-PAGE and immunoblotting, genomic DNA isolation, polymerase chain reaction, DNA sequencing. 5. Analysis of mutational status of gene of interest, finnalization of individual protocols.
Literature
  • YAMAMOTO, T. Targeted Genome Editing Using Site-Specific Nucleases, ZFNs, TALENs, and the CRISPR/Cas9 system. 2015. Springer. 205 pp. ISBN 978-4-431-55226-0.
  • MOULDY, S. RNA Interference Challenges and Therapeutic Opportunities. 2015. New York : Humana Press : Springer. ISBN: 978-1-4939-1537-8.
  • GREEN, Michael R. and Joseph SAMBROOK. Molecular cloning : a laboratory manual. 4th ed. New York [N.Y.]: Cold Spring Harbor Laboratory Press, 2012, xxxiii, s. ISBN 9781936113422. info
Teaching methods
Introductory lecture, individual written project prepared by students followed by practical laboratory training, class discussion.
Assessment methods
Credits given for project preparation, participation in practical lessons and experimental data processing and analysis.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
spring 2012 - acreditation

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)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
doc. RNDr. Jakub Neradil, Ph.D. (seminar tutor)
Mgr. Lucia Knopfová, Ph.D. (seminar tutor)
Mgr. Andrea Fořtová, Ph.D. (seminar tutor)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligaes; to perform separation of DNA molecules by agarose gel electrophoresis to elute DNA molecules out of a agarose gels At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Teaching methods
Brief lecture follwed by practical laboratory training.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2011 - only for the accreditation
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skills in microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Main objectives can be summarized as follows: to learn the basic techniques of DNA manipulation in vitro to obtain recombinant DNA molecules to learn the ways of successful purification of plasmid DNA from bacterial cells; to cut the purified plasmid DNA using various restriction enzymes; to become familiar with approaches to modify recessed termini of DNA to seal DNA molecules using DNA ligaes; to perform separation of DNA molecules by agarose gel electrophoresis to elute DNA molecules out of a agarose gels At the end of the course students should be able to perform these experiments independently and to applied in correct way to address specific biological phenomena.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Teaching methods
Brief lecture follwed by practical laboratory training.
Assessment methods
Credits are given for active work at a bench, for participation in each lesson and for elaborating detailed protocols of each step of the procedure used, including results and conclusions obtained.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.

Bi6405 Methods of Molecular Biology - practice

Faculty of Science
Spring 2008 - for the purpose of the accreditation
Extent and Intensity
0/3/0. 3 credit(s). Type of Completion: z (credit).
Teacher(s)
prof. RNDr. Jan Šmarda, CSc. (seminar tutor)
prof. Mgr. Petr Beneš, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jan Šmarda, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Jan Šmarda, CSc.
Prerequisites
( Ex_3065 Molekulární biologie || Imp_9115 Molekulární biologie || B3120 Molecular and cell biology || B4030 Molecular biology || B5740 Molecular biology || B6130 Molecular biology || B7940 Molecular biology || B4020 Molecular biology || Bi4020 Molecular biology || Bi4035 Molecular biology - lab.pract. ) && NOW( Bi6400 Methods of molecular biology ) && ! B6405 Molecular Methods - practice
The course requires basic practical skils from microbiology, biochemistry and molecular biology as, for example, preparation of buffers, cultivation media, sterile liquide handling, inoculation, centrifugation and so on.
Course Enrolment Limitations
The course is only offered to the students of the study fields the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course acquire experience with DNA molecule manipulations in vitro to obtain recombinant DNA molecules. The aim of the course is to teach the ways of successful purification of pure plasmid DNA from bacterial cells, its fragmentation using various restriction enzymes, modifications of DNA termini and ligation with other DNA molecules. In addition, students get experience with DNA electrophoresis and gel elution.
Syllabus
  • 1. Inoculation and cultivation of bacterial cells having appropriate plasmids. 2. Isolation of plasmid DNA from bacterial cells using Qiagen columns. 3. Restriction analysis of plasmid DNA and modification of 5 overhang termini using DNA polymerase. 4. Agarose electrophoresis of fragmented DNA. 5. Elution of appropriate fragments from a gel. 6. Ligation of appropriate DNA molecules. 7. Transformation of competent bacterial cells with ligation mixture. 8. Selection of transformants. 9. Screening of transformants for the presence of recombinant plasmid (plasmid minipreparation, restriction analysis, electrophoresis).
Literature
  • SAMBROOK, J., E.F. FRITSCH and T. MANIATIS. Molecular Cloning. A laboratory Manual. Second Edition. Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989. ISBN 0-87969-309-6. info
Assessment methods (in Czech)
zápočet se udílí za aktivní přístup, účast ve výuce a vypacování kvalitních protokolů z jednotlivých úloh.
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.
  • Enrolment Statistics (recent)