User:Loguej
Education:
B.S. in molecular, cellular and developmental biology with minors in organic and biochemistry from the University of Oregon, Eugene, OR
Currently pursuing a Ph.D. in biochemistry and molecular biology from Oregon Health and Sciences University, Portland, OR
Thesis mentor Dr. Richard H. Goodman
Thesis project:
Molecular mechanism of neurite outgrowth by microRNA-132.
Publications:
Mooers, BH, Logue, JS, Berglund, JA "The structural basis of myotonic dystrophy from the crystal structure of CUG repeats" (2005) PNAS Nov 15;102(46):16626-31.
Contact:
loguej AT ohsu DOT edu
Homework and Questions:
DNA Replication - Week 2
Lopes et al
Despite the remarkable discovery that DNA polymerase can transcribe through UV lesions when yeast cells lack NER, list potential genotoxic consequences of transcribing through these lesions?
Answer:
Leaving behind DNA lesions and ssDNA, poses many problems to the cell. The lack of nucleotide excision repair is sufficient to introduce mutations into the genome by mis-pairing to DNA UV-adducts. Additionally, ssDNA gaps that are filled in post-replication, would be expected to have abberant chromatin structure, according to current models of DNA replication and chromatin structure. Current models suggests nucleosomes are added during replication, and subsequently modified. Filled in ssDNA post-replication, would likely produce hypersensitive sites, if in the right place, this could dramatically upregulate a gene. It would be interesting to know whether nucleosomes at these sites can be added post-replication, or if neighboring nucleosomes can slide and fill in the gaps to allow for proper chromatin stucture.
Heller and Marians
Why might the mechanism described by Heller and Marians be considered heretical?
Answer:
The mechanism proposed by Heller and Marians could certainly be considered heretical. The mechanism proposed, where DNAG primase fills in ssDNA gaps post replication suggests DNAG can act independently of the transcription machinery. DNAG is most often associated with the lagging strand during DNA replication, acting in concert with the replication fork and replication machinery. This mechanism suggests DNAG can be recruited to ssDNA independent of the replication machinery, and independent of an origin of replication, of which is tightly regulated. This mechanism in some ways shatters the current models of DNA replication and repair, and revives old ones. The work by Heller and Marians redefines the functionality of DNAG, and mechanisms of repair.
Moyer et al
1. If the purification strategy in figure 1A hadn't been so stringent, what other kinds of factors might of been isolated with cdc45?
Answer:
The stringent purification used in Moyer et al not suprisingly isolated a core helicase complex. A less stringent approach may have identified new components of the replication or pre-replication machinery like cdt-1. Mass spectrometry based approaches to identify new protein partners or complexes is a compromise between isolating tightly bound proteins or loose or transient partners, the latter can often produce false positives since this requires gentle conditions.
2. What does figure 5 prove?
Answer:
Figure 5 demonstrates that cdc45 is necessary for S-phase progression. The others suggest this shows that cdc45 is a necessary component of the replication machinery in vivo, but cdc45 may also trigger the S/M cell cycle check point. Further experiments in vivo are necessary to prove that cdc45 is a component of the replication machinery. Co-localization, for example, of cdc45 using replication specific antibodies towards polII on a replicating chromosome may provide further evidence.
