Download General review themes in red

BMP5747 Molecular Parasitology
Structure of the lessons: Two papers per session and sometimes one
general review of a theme (textbook/review based)
You should present the paper as a talk presenting as if they were the
authors but maintain a critical eye for lapses and errors
You are chosen by rolling the dice – general review presenters are
chosen in advance and don´t need to present paper at that day.
Unprepared papers cost 1 point penalty of you final grade.
It´s about understanding the stuff: If in doubt about any detail, mark
it up in your presentation and let your colleagues (and me) explain if
possible
One final (written) exam about themes and techniques treated in the
papers
15.9. General intro: DNA replication (Chapter Genes 10) Classic paper: Replication of
kinetoplast DNA maxicircles. Hajduk, Klein, Englund, Cell Volume 36, Issue 2,
p483–492, February 1984 / Identification of ORC1/CDC6-interacting factors in
Trypanosoma brucei reveals critical features of origin recognition complex
architecture. PLoS One. 2012;7(3):e32674. doi: 10.1371/journal.pone.0032674.
Epub 2012 Mar 8.
20.9. Introducing mutations during replication: DNA secondary structures are
associated with recombination in major Plasmodium falciparum variable
surface antigen gene families. Nucleic Acids Res. 2014 Feb;42(4):2270-81. doi:
10.1093/nar/gkt1174. Epub 2013 Nov 18.
How to find startpoints of replication in the apicoplast: Multiple replication
origins within the inverted repeat region of the Plasmodium falciparum
apicoplast genome are differentially activated. Mol Biochem Parasitol. 2005
Jan;139(1):99-106.
22.9. What to do with chromosome ends: Telomerase background Intro, Articles: The
unusually large Plasmodium telomerase reverse-transcriptase localizes in a
discrete compartment associated with the nucleolus. Nucleic Acids Res. 2005
Feb 18;33(3):1111-22. Telomere length affects the frequency and mechanism
of antigenic variation in Trypanosoma brucei. PLoS Pathog. 2012;8(8):
e1002900. doi: 10.1371/journal.ppat.1002900.
27.9. Genomics: Working with genome databases: TriTryp e PlasmoDB. High througput
sequencing with new techniques (PacBio sequencer): Show principle of this
sequencing technique and give a general idea about the results: Genome
Announc. 2016 Sep 1;4(5). pii: e00883-16. doi: 10.1128/genomeA.00883-16. ...
Continued: High-Quality Genome Assembly and Annotation for Plasmodium
coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology.
29.9. 2016: Transcription: General mode of transcription initiation and transcript
maturation in eucaryotes. Classic paper: Identification of a novel Y branch
structure as an intermediate in trypanosome mRNA processing: evidence for
trans splicing. Cell. 1986 Nov 21;47(4):517-25. Variant gene transcription in
Plasmodium falciparum, classic paper : Antigenic variation in malaria: in situ
switching, relaxed and mutually exclusive transcription of var genes during intraerythrocytic development in Plasmodium falciparum. EMBO J. 1998 Sep
5;17(18):5418-26.
4.10. 2016: RNAi, siRNAs, shRNA, miRNAs etc. : RNA interference Small RNAs:
Trans-acting GC-rich non-coding RNA at var expression sites modulates gene
counting in malaria parasite NAR doi: 10.1093/nar/gkw664
Variant gene transcription in Giardia lamblia: Antigenic variation in Giardia
lamblia is regulated by RNA interference. Nature. 2008 Dec 11;456(7223):750-4.
6. 10. 2016: Control of translation of already made transcripts : P-bodies and
untranslated ORFs. The RNA helicase DHH1 is central to the correct expression of
many developmentally regulated mRNAs in trypanosomes. J Cell Sci. 2010 Mar
1;123(Pt 5):699-711. doi: 10.1242/jcs.058511. Epub 2010. An upstream open
reading frame controls translation of var2csa, a gene implicated in placental
malaria. PLoS Pathog. 2009 Jan;5(1):e1000256. doi: 0.1371/journal.ppat.1000256.
Epub 2009 Jan 2.
11.10.2016: Epigenetics: the role of histone modification. A histone
methyltransferase modulates antigenic variation in African trypanosomes. PLoS
Biol. 2008 Jul 1;6(7):e161. doi: 10.1371/journal.pbio.0060161.
Cont. 6.10.2016: H2A.Z demarcates intergenic regions of the plasmodium falciparum
epigenome that are dynamically marked by H3K9ac and H3K4me3. PLoS Pathog. 2010
Dec 16;6(12):e1001223. doi: 10.1371/journal.ppat.1001223.
13.10.2016: Novel tools: Genomic editing with Zincfinger Nuclease and CRISPR/CAS9
editing Applications: CRISPR-Cas9-Mediated Genome Editing in Leishmania donovani
mBio. 2015 Jul-Aug; 6(4): e00861-15. A Genome-wide CRISPR Screen in Toxoplasma
Identifies Essential Apicomplexan Genes. Cell. 2016 Sep 8;166(6):1423-1435.e12. doi:
10.1016/j.cell.2016.08.019. Epub 2016 Sep 2.
(General review themes in red)
18.10.2016 Final Exam
Example of a prepared paper
Goal of the study:
Develop and test a new vector set for CAS9 mediated genome manipulation in P.
falciparum
Background:
• Until now, plasmids containing the homology regions and the cassette for the
trc/sgRNA were on one plasmid and the CAS9 enzyme on a second
• this impossibilitates subsequent manipulations since significant parts of the
homology-region containing plasmid integrate in the genome
• Drug resistance genes also get integrated
Published system for P. falciparum:
Strategy of the authors, using plasmids from the previous study by Ghorbal and colleagues
Why did they use the SET2 locus?
SET2 is a chromatin modifier but can be deleted without large effects on parasite growth
Sequence is successfully modified
CAS9 expressing parasites become green
Etc.