Course Information

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
RNDr. Hana Konečná (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

Fri 8:00–9:50 B11/306

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 8 fields of study the course is directly associated with, display

Course objectives

At the end of the course, student will acquire theory of basic approaches in current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.

Syllabus

• Introduction to genomics.
• Methods of functional genomics.
• Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR).
• In silico prediction of gene functions.
• Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
• Fragmental DNA analyzis and positional cloning as tools in forward genetics.
• Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
• Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
• Southern blot and DNA molecular hybridization.
• Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
• Methods for the gene expression analysis (qualitative and quantitaive gene expression profiling, Genevestigator, transaltional and transcriptional fusions with reporter gene).
• New approaches: Chemical genetics.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Teaching methods

The main teaching method are lectures that include particular examples from the own scientific praxis and demonstration of the solution of particular problems via individual tools of functional genomics.

Assessment methods

Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials available on-line are rather supporting. Type of exam: Written exam.

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
RNDr. Hana Konečná (lecturer)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Timetable

Fri 12:00–13:50 B11/306

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 7 fields of study the course is directly associated with, display

Course objectives

At the end of the course, student will acquire theory of basic approaches in current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.

Syllabus

• Introduction to genomics.
• Methods of functional genomics.
• Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR).
• In silico prediction of gene functions.
• Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
• Fragmental DNA analyzis and positional cloning as tools in forward genetics.
• Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
• Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
• Southern blot and DNA molecular hybridization.
• Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
• Methods for the gene expression analysis (qualitative and quantitaive gene expression profiling, Genevestigator, transaltional and transcriptional fusions with reporter gene).
• New approaches: Chemical genetics.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Teaching methods

The main teaching method are lectures that include particular examples from the own scientific praxis and demonstration of the solution of particular problems via individual tools of functional genomics.

Assessment methods

Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials available on-line are rather supporting. Type of exam: Written exam.

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
Mgr. Jakub Horák, Dr. rer. nat. (lecturer)
RNDr. Hana Konečná (lecturer)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Timetable

Wed 12:00–13:50 B11/306

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

At the end of the course, student will acquire theory of basic approaches in current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.

Syllabus

• Introduction to genomics.
• Methods of functional genomics.
• Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR).
• In silico prediction of gene functions.
• Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
• Fragmental DNA analyzis and positional cloning as tools in forward genetics.
• Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
• Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
• Southern blot and DNA molecular hybridization.
• Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
• Methods for the gene expression analysis (qualitative and quantitaive gene expression profiling, Genevestigator, transaltional and transcriptional fusions with reporter gene).
• New approaches: Chemical genetics.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Teaching methods

The main teaching method are lectures that include particular examples from the own scientific praxis and demonstration of the solution of particular problems via individual tools of functional genomics.

Assessment methods

Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials available on-line are rather supporting. Type of exam: Written exam.

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
RNDr. Hana Konečná (lecturer)
Mgr. Eva Paděrová (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Timetable

Fri 8:00–9:50 BR3

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

At the end of the course, student will acquire theory of basic approaches in current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.

Syllabus

• Introduction to genomics.
• Methods of functional genomics.
• Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR).
• In silico prediction of gene functions.
• Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
• Fragmental DNA analyzis and positional cloning as tools in forward genetics.
• Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
• Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
• Southern blot and DNA molecular hybridization.
• Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
• Methods for the gene expression analysis (qualitative and quantitaive gene expression profiling, Genevestigator, transaltional and transcriptional fusions with reporter gene).
• New approaches: Chemical genetics.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Teaching methods

The main teaching method are lectures that include particular examples from the own scientific praxis and demonstration of the solution of particular problems via individual tools of functional genomics.

Assessment methods

Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials available on-line are rather supporting. Type of exam: Written exam.

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
RNDr. Hana Konečná (lecturer)
Mgr. Eva Paděrová (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Timetable

Fri 10:00–11:50 BR3

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

Student will acquire theory of basic approaches current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.

Syllabus

• Introduction to genomics.
• Methods of functional genomics.
• Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR).
• In silico prediction of gene functions.
• Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
• Fragmental DNA analyzis and positional cloning as tools in forward genetics.
• Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
• Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
• Southern blot and DNA molecular hybridization.
• Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
• Methods for the gene expression analysis (qualitative and quantitaive gene expression profiling, Genevestigator, transaltional and transcriptional fusions with reporter gene).
• New approaches: Chemical genetics.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Assessment methods

Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials available on-line are rather supporting. Type of exam: Written exam.

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
RNDr. Hana Konečná (lecturer)
Mgr. Eva Paděrová (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Timetable

Fri 8:00–9:50 BR3

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

Student will acquire theory of basic approaches current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory.

Syllabus

• Introduction to genomics. Methods of functional genomics. Genome databases and basic tools of bioinformatics (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], searche in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR). In silico prediction of gene functions. Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference). Fragmental DNA analyzis and positional cloning as tools in forward genetics. Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion). Phenotypic profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches). Southern blot and DNA molecular hybridization. Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Assessment methods (in Czech)

přednáška, ukončena (klasifikovaným) zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Timetable

Fri 7:00–8:50 BR3

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

Student will acquire theory of basic approaches current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory.

Syllabus

• Introduction to genomics. Methods of functional genomics. Genome databases and basic tools of bioinformatics (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], searche in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR). In silico prediction of gene functions. Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference). Fragmental DNA analyzis and positional cloning as tools in forward genetics. Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion). Phenotypic profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches). Southern blot and DNA molecular hybridization. Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Assessment methods (in Czech)

přednáška, ukončena (klasifikovaným) zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: graded credit. Other types of completion: z (credit).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Timetable

Fri 8:00–9:50 B1,01004

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

Student will acquire theory of basic approaches current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory.

Syllabus

• Introduction to genomics. Methods of functional genomics. Genome databases and basic tools of bioinformatics (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], searche in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR). In silico prediction of gene functions. Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference). Fragmental DNA analyzis and positional cloning as tools in forward genetics. Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion). Phenotypic profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches). Southern blot and DNA molecular hybridization. Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Assessment methods (in Czech)

přednáška, ukončena (klasifikovaným) zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

The course is taught annually.

Bi7201 Genomics - a basic course

Extent and Intensity

1/2/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Břetislav Brzobohatý, CSc. (lecturer)
RNDr. Eliška Nejedlá, CSc. (seminar tutor)
RNDr. Alena Kuderová, CSc. (seminar tutor)
RNDr. Hana Konečná (seminar tutor)
doc. RNDr. Jan Hejátko, Ph.D. (seminar tutor)
Mgr. Eva Paděrová (seminar tutor)
Mgr. Markéta Pernisová, Ph.D. (assistant)
Nagavalli Subbanna Kiran, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Břetislav Brzobohatý, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Břetislav Brzobohatý, CSc.

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology is a prerequisite for subscription to the course.

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 36 student(s).
Current registration and enrolment status: enrolled: 0/36, only registered: 0/36, only registered with preference (fields directly associated with the programme): 0/36

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

Students will acquire a working knowledge of genomic databases and their applications in experimental analysis of biological functions of genes and genomes. Biological function of a concrete member of a complex gene family will be analysed by identification of an insertion mutation in the gene and analysis of phenotype alterations in the mutant.

Syllabus

• Introduction to genomics. Methods of functional genomics. Genome databases. Insertion mutant collections - a powerful tool for plant functional genomics. DNA fragment analysis - automated genetic analyzer ABI PRISM 310. Oligonucleotide design, synthesis and purification - EXPEDITE 8909 Nucleic Acid Synthesizer. Genomic DNA isolation from Arabidopsis thaliana. PCR, DNA electrophoresis in agarose gels. Southern blot and DNA molecular hybridization. Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Assessment methods (in Czech)

blokové praktikum, ukončeno (klasifikovaným) zápočtem

Language of instruction

Czech

Follow-Up Courses

• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: in blocks.
Information on the extent and intensity of the course: 1 týden.

Bi7201 Genomics - a basic course

Extent and Intensity

1/2/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Břetislav Brzobohatý, CSc. (lecturer)
RNDr. Eliška Nejedlá, CSc. (seminar tutor)
RNDr. Alena Kuderová, CSc. (seminar tutor)
RNDr. Hana Konečná (seminar tutor)
doc. RNDr. Jan Hejátko, Ph.D. (seminar tutor)
Mgr. Markéta Pernisová, Ph.D. (assistant)
Nagavalli Subbanna Kiran, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Břetislav Brzobohatý, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Břetislav Brzobohatý, CSc.

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology is a prerequisite for subscription to the course.

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 36 student(s).
Current registration and enrolment status: enrolled: 0/36, only registered: 0/36, only registered with preference (fields directly associated with the programme): 0/36

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

Students will acquire a working knowledge of genomic databases and their applications in experimental analysis of biological functions of genes and genomes. Biological function of a concrete member of a complex gene family will be analysed by identification of an insertion mutation in the gene and analysis of phenotype alterations in the mutant.

Syllabus

• Introduction to genomics. Methods of functional genomics. Genome databases. Insertion mutant collections - a powerful tool for plant functional genomics. DNA fragment analysis - automated genetic analyzer ABI PRISM 310. Oligonucleotide design, synthesis and purification - EXPEDITE 8909 Nucleic Acid Synthesizer. Genomic DNA isolation from Arabidopsis thaliana. PCR, DNA electrophoresis in agarose gels. Southern blot and DNA molecular hybridization. Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Assessment methods (in Czech)

blokové praktikum, ukončeno (klasifikovaným) zápočtem

Language of instruction

Czech

Follow-Up Courses

• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: in blocks.
Information on the extent and intensity of the course: 1 týden.

Bi7201 Genomics - a basic course

Extent and Intensity

1/2/0. 3 credit(s). Type of Completion: z (credit).

Teacher(s)

prof. RNDr. Břetislav Brzobohatý, CSc. (lecturer)
doc. Ing. Matej Lexa, Ph.D. (seminar tutor)
RNDr. Eliška Nejedlá, CSc. (seminar tutor)
RNDr. Hana Konečná (seminar tutor)
Mgr. Hana Bubeníčková (assistant)

Guaranteed by

prof. RNDr. Břetislav Brzobohatý, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Břetislav Brzobohatý, CSc.

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology is a prerequisite for subscription to the course.

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 24 student(s).
Current registration and enrolment status: enrolled: 0/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24

fields of study / plans the course is directly associated with

• Biophysics (programme PřF, M-FY)
• Biochemistry (programme PřF, M-CH)
• Environmental Chemistry (programme PřF, M-CH)
• Molecular Biology and Genetics (programme PřF, M-BI)
• General Biology (programme PřF, M-BI)

Course objectives

Students will acquire a working knowledge of genomic databases and their applications in experimental analysis of biological functions of genes and genomes. Biological function of a concrete member of a complex gene family will be analysed by identification of an insertion mutation in the gene and analysis of phenotype alterations in the mutant.

Syllabus

• Introduction to genomics. Methods of functional genomics. Genome databases. Insertion mutant collections - a powerful tool for plant functional genomics. DNA fragment analysis - automated genetic analyzer ABI PRISM 310. Oligonucleotide design, synthesis and purification - EXPEDITE 8909 Nucleic Acid Synthesizer. Genomic DNA isolation from Arabidopsis thaliana. PCR, DNA electrophoresis in agarose gels. Southern blot and DNA molecular hybridization. Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Assessment methods (in Czech)

blokové praktikum, ukončeno (klasifikovaným) zápočtem

Language of instruction

Czech

Follow-Up Courses

• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: in blocks.
Information on the extent and intensity of the course: 1 týden.

Bi7201 Genomics - a basic course

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
RNDr. Hana Konečná (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

• Biophysics (programme PřF, N-FY)
• Biochemistry (programme PřF, N-BCH)
• Environmental Chemistry (programme PřF, N-CH)
• Molecular Biology and Genetics (programme PřF, N-BI)
• General Biology (programme PřF, N-BI)

Course objectives

At the end of the course, student will acquire theory of basic approaches in current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.

Syllabus

• Introduction to genomics.
• Methods of functional genomics.
• Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR).
• In silico prediction of gene functions.
• Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
• Fragmental DNA analyzis and positional cloning as tools in forward genetics.
• Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
• Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
• Southern blot and DNA molecular hybridization.
• Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
• Methods for the gene expression analysis (qualitative and quantitaive gene expression profiling, Genevestigator, transaltional and transcriptional fusions with reporter gene).
• New approaches: Chemical genetics.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Teaching methods

The main teaching method are lectures that include particular examples from the own scientific praxis and demonstration of the solution of particular problems via individual tools of functional genomics.

Assessment methods

Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials available on-line are rather supporting. Type of exam: Written exam.

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

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

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)
RNDr. Hana Konečná (lecturer)
Mgr. Eva Paděrová (lecturer)
Mgr. et Mgr. Veronika Oškerová, Ph.D. (assistant)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

At the end of the course, student will acquire theory of basic approaches in current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory. At the end of this course, students get an overview of modern approaches of functional genomics. Students will be able to use and interpret information deposited in genomic databases and they will be oriented in the modern biology approaches and problems. Student will be able to contribute in a creative way to the further development of modern biology.

Syllabus

• Introduction to genomics.
• Methods of functional genomics.
• Genome databases and basic tools of bioinformatics: (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], search in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR).
• In silico prediction of gene functions.
• Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference).
• Fragmental DNA analyzis and positional cloning as tools in forward genetics.
• Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion).
• Phenotype profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches).
• Southern blot and DNA molecular hybridization.
• Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.
• Methods for the gene expression analysis (qualitative and quantitaive gene expression profiling, Genevestigator, transaltional and transcriptional fusions with reporter gene).
• New approaches: Chemical genetics.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Teaching methods

The main teaching method are lectures that include particular examples from the own scientific praxis and demonstration of the solution of particular problems via individual tools of functional genomics.

Assessment methods

Type of lectures: The lectures are facultative, however, the presence of students is highly desirable for complete understanding of principles of functional genomics approaches; the teaching materials available on-line are rather supporting. Type of exam: Written exam.

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

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

Bi7201 Genomics - a basic course

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).

Teacher(s)

doc. RNDr. Jan Hejátko, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Jan Hejátko, Ph.D.

Prerequisites

Completion of basic courses of biochemistry and/or molecular biology and genetics is a prerequisite for subscription to the course.

Course Enrolment Limitations

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

fields of study / plans the course is directly associated with

there are 10 fields of study the course is directly associated with, display

Course objectives

Student will acquire theory of basic approaches current functional genomics: Theory of basic bioinformatics tools, basics of the work with genomic databases, identification of gene function using in silico approach, targeted gene silencing and gain of function approaches, phenotype profiling (DNA, RNA and protein chips), identification and analysis of sequence specific mutants, fragmental analysis and positional cloning, etc.. Lectures are conceived as an extended introduction into practical courses (Bi7201c), in frame of which students will be able to practice most of the theory.

Syllabus

• Introduction to genomics. Methods of functional genomics. Genome databases and basic tools of bioinformatics (types of databases, databases search, finding of similar sequences [BLAST and FASTA], multiple sequence alignment [CLUSTALW], searche in genomic databases of Arabidopsis thaliana, localization of genes on chromozomes, identification and analyzis of promoter regions of individual genes [ALIBABA], virtual PCR). In silico prediction of gene functions. Forward and reverse genetics approaches (methods of the identification of sequence specific mutants, mutant collections and their analyzis, physical and chemical mutagenesis, targeted gene silencing using RNA interference). Fragmental DNA analyzis and positional cloning as tools in forward genetics. Gain of function approaches in identification of the gene function (activation T-DNA mutagenesis, ectopic overexpression, regulated gene expresion). Phenotypic profiling (cDNA, RNA and protein chips, metabolic profiling, microdissection, proteomic approaches). Southern blot and DNA molecular hybridization. Identification and characterization of an insertion mutation in a selected member of a complex gene family in Arabidopsis thaliana via a PCR based screen.

Literature

• Hunt, S.P., Livesey, F.J. (Editors). Functional Genomics : A Practical Approach. Practical Approach Series
• Starkey, M.P., and Elaswarapu R. (Editors). Genomics Protocols. Methods in Molecular Biology, Vol 175

Assessment methods (in Czech)

přednáška, ukončena (klasifikovaným) zápočtem

Language of instruction

Czech

Follow-Up Courses

• Bi7201c Genomics - practice
• Bi8930 Developmental and cellular biology of plants
• B8202 Proteomics - a basic course

Further comments (probably available only in Czech)

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

• Enrolment Statistics (recent)