Učni načrt predmeta

Predmet:
Evolucijska genomika
Course:
Evolutionary Genomics
Študijski program in stopnja /
Study programme and level
Študijska smer /
Study field
Letnik /
Academic year
Semester /
Semester
Nanoznanosti in nanotehnologije, 3. stopnja Bioznanosti 1 1
Nanosciences and Nanotechnologies, 3rd cycle Biosciences 1 1
Vrsta predmeta / Course type
Izbirni / Elective
Univerzitetna koda predmeta / University course code:
NANO3-797
Predavanja
Lectures
Seminar
Seminar
Vaje
Tutorial
Klinične vaje
work
Druge oblike
študija
Samost. delo
Individ. work
ECTS
30 30 30 210 5

*Navedena porazdelitev ur velja, če je vpisanih vsaj 15 študentov. Drugače se obseg izvedbe kontaktnih ur sorazmerno zmanjša in prenese v samostojno delo. / This distribution of hours is valid if at least 15 students are enrolled. Otherwise the contact hours are linearly reduced and transfered to individual work.

Nosilec predmeta / Course leader:
prof. dr. Dušan Kordiš
Sodelavci / Lecturers:
Jeziki / Languages:
Predavanja / Lectures:
slovenščina, angleščina / Slovenian, English
Vaje / Tutorial:
Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:
Prerequisites:

Predznanje biologije, genetike in biokemije je potrebno za študij in razumevanje procesov v bioloških sistemih.

Knowledge in biology, genetics and biochemistry acquired at the undergraduate level.

Vsebina:
Content (Syllabus outline):

- Kaj je genom?
- Razumevanje genomskih zaporedij
- Anatomija eukariontskih in prokariontskih genomov
- Regulacija delovanja genoma
- Struktura in dinamika genomov in proteomov
- Molekularni vzroki evolucije genomov
- Vzorci genomske evolucije
- Filogenetika in filogenomika
- Evolucija proteinov

Laboratorijske vaje (računalniške):
- Genomske podatkovne baze
- Specializirane proteomske databaze
- Evolucijske analize genomskih sekvenc
- Evolucijske analize proteomov

- What is a genome?
- Understanding a genome sequence
- Genome anatomies (eukaryotes vs prokaryotes)
- Regulation of genome activity
- Structure and dynamics of genomes and proteomes
- Molecular basis of genome evolution
- Paterns of genome evolution
- Molecular phylogenetics and phylogenomics
- Protein evolution

Laboratory work (computational):
- Genome databases
- Protein and proteome databases
- Evolutionary analyses of genome sequences
- Evolutionary analyses of proteomes

Temeljna literatura in viri / Readings:

- Brown, T.A. (2017) Genomes. 4th Edition, Garland Science.
- Caetano‐Anollés, G. (2010) Evolutionary Genomics and Systems Biology. Wiley‐Blackwell.
- Pagel, M. & Pomiankowski A. (2008) Evolutionary Genomics and Proteomics. Sinauer.
- Lynch, M. (2007) The Origins of Genome Architecture. Sinauer.

Cilji in kompetence:
Objectives and competences:

Študenti pridobijo znanje o organizaciji, delovanju in analizi celotnih genomov (prokariontskih in evkariontskih) z evolucijskega vidika, pomen razumevanja informacij, ki so skrite v genomskih sekvencah, ter mehanizmov in vzorcev evolucije genomov. Študenti bodo spoznali in uporabljali specializirane genomske in proteomske podatkovne baze ter metode molekularne evolucije za prepoznavanje in ovrednotenje evolucije posameznih genomskih komponent.

Splošne kompetence:
- obvladanje raziskovalnih metod, postopkov in procesov, razvoj kritične in samokritične presoje;
- razvoj sposobnosti uporabe znanja v praksi;
- razvoj komunikacijskih sposobnosti in spretnosti, posebej komunikacije v mednarodnem okolju;
- kooperativnost, delo v skupini (in v mednarodnem okolju).

Predmetno-specifične kompetence:
Študij tega predmeta je nujna podlaga za to, da bo študent razumel, kako se genomi in njegove komponente spreminjajo s časom. Predstavljene raziskovalne metode bodo študenti lahko uporabljali na različnih strokovnih področjih. Pridobljeno znanje jim bo pomagalo pri uporabi izjemno kompleksnih genomskih podatkov pri reševanju različnih problemov iz sodobne biologije ter pri interpretaciji rezultatov, pridobljenih iz genomskih in proteomskih podatkovnih baz.

Students will acquire a thorough understanding of genome organization and activity, of complete genome analysis (prokaryotic and eukaryotic), and mechanisms and patterns of genome evolution. Students will be able to extract and understand the enormous amount of information that is hidden in genome sequences. Students will learn how to use the specialized genome and proteome databases, and diverse approaches that are necessary for the evolutionary analyses of different genome components.

General Competences:
- the student will master research methods, procedures and processes and develop skills to critically asses his activities;
- the student will develop skills to transfer the ideas from the basic knowledge pool into applications;
- the student will develop communications skills to present research achievement in the international environment;
- training for team work (in international environment).

Course Specific Competences:
This course prepares students to work on the evolutionary analysis of complex genome data. Students will understand how and why the genomes and genome components change in time. Students can use acquired research methods in different fields of life sciences. Acquired knowledge will enable students to use very complex genome data in solving different problems in modern biology and to understand the results obtained from the analysis of the genome and proteome databases.

Predvideni študijski rezultati:
Intendeded learning outcomes:

Znanje in razumevanje:
Študent pri predmetu pridobi znanje o nastanku, strukturni organizaciji, delovanju, regulaciji in evoluciji genomov. Pridobljeno znanje omogoča študentom razumevanje izjemno kompleksnih genomskih podatkov. Študent se nauči uporabljati genomske podatkovne baze.

Uporaba:
Študij tega predmeta je nujna podlaga za to, da bo študent razumel, kako se genomi in njegove komponente spreminjajo s časom. Predstavljene raziskovalne metode bodo študenti lahko uporabljali na različnih strokovnih področjih. Pridobljeno znanje jim bo pomagalo pri uporabi izjemno kompleksnih genomskih podatkov pri reševanju različnih problemov iz sodobne biologije ter pri interpretaciji rezultatov, pridobljenih iz genomskih podatkovnih baz.

Refleksija:
Študent pridobi sposobnost kompleksnega biološkega načina razmišljanja in razvije zmožnost abstraktne predstave o organizaciji, delovanju in evoluciji genomov.

Prenosljive spretnosti:
Izkušnje pri reševanju problemov. Timsko delo (pri vajah). Zbiranje in interpretiranje rezultatov ter njihovo kritično vrednotenje. Uporaba tuje literature. Podajanje poročil o opravljenem delu.

Knowledge and Comprehension:
Students will acquire knowledge about the origin, structural organization, functioning, regulation and evolution of genomes. This will enable them to understand the extremely complex genomic data. Students will learn how to use genomic databases.

Application
The course gives students the indispensable basis for the understanding of the evolution of genomes and their components. Students will be able to apply research methods presented during the course to various research fields. The acquired knowledge will help them to use the highly complex genomic data when solving various problems of modern biology, as well as to interpret the results obtained from genomic and proteomic databases.

Analysis
Students will develop the ability to complex biological thinking, as well as the capacity for the abstraction of genome organization, functioning and evolution.

Skill-transference Ability
Problem-solving skills. Teamwork (at Laboratory work). Obtaining and interpreting results and their critical evaluation. Use of scientific literature. Writing reports on the practical work performed.

Metode poučevanja in učenja:
Learning and teaching methods:

Predavanja, seminarji, konzultacije

Lectures, seminars, consultations

Načini ocenjevanja:
Delež v % / Weight in %
Assesment:
Seminar
50 %
Seminar
Ustni izpit
50 %
Oral exam
Reference nosilca / Lecturer's references:
1. Kordiš D, Turk V. (2023). Origin and Early Diversification of the Papain Family of Cysteine Peptidases. Int J Mol Sci. 24:11761.
2. Zupanič N, Počič J, Leonardi A, Šribar J, Kordiš D, Križaj I. (2023). Serine pseudoproteases in physiology and disease. FEBS J. 290:2263-2278.
3. Kostanjšek R, Diderichsen B, Recknagel H, Gunde-Cimerman N, Gostinčar C, Fan G, Kordiš D, Trontelj P, Jiang H, Bolund L, Luo Y. (2022). Toward the massive genome of Proteus anguinus-illuminating longevity, regeneration, convergent evolution, and metabolic disorders. Ann N Y Acad Sci. 1507:5-11.
4. Ott Rutar S, Kordiš D. (2020). Analysis of the RNA virome of basal hexapods. PeerJ. 8:e8336.
5. Feliciello I, Pezer Ž, Kordiš D, Bruvo Mađarić B, Ugarković Đ. (2020). Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin. Genome Biol Evol. 12:2125-2138.