Random Records

Note for: Impact of DNA repair pathways on the cytotoxicity of piperlongumine in chicken DT40 cell-lines (doi: 10.18632/genesandcancer.26) One of the paper which was cited by this one, has just been retracted recently (2018, Sep -- Selective killing of cancer cells by a small molecule targeting the stress response to ROS. Nature.  2011;475:231-4 ). It was the original work which showed that Piperlongumine can generate ROS which eventually was the major mechanism killing the cancer cell lines. Piperlongumine induces ROS. Aim; examine the contribution of ROS-induced DNA damage to the cytotoxicity by piperlongumine. Method; various DNA repair-deficient chicken DT40 cell-lines with a single DNA repair gene deletion were tested for cellular sensitivity to piperlongumine. ROS is necessary for several physiological responses, including differentiation, immunity, metabolic adaptation and autophagy. A fine balance between the production of ROS and the detoxifi...

Note for: Cooperative Roles of Vertebrate Fbh1 and Blm DNA Helicases in Avoidance of Crossovers during Recombination Initiated by Replication Fork Collapse (doi: 10.1128/MCB.02043-06) Fbh1 (F-box DNA helicase 1) -- treating with the DNA damaging agents; no prominent phenotype, contradict with yeast -- there might be the compensate pw in DT40. FBH(-/-) phenotype in DT40; 1.increase sister chromatid exchange 2.formation of radial structures 3.prevent extensive strand exchange during HR 4.work with Bloom helicase - controling recombination-mediated DSB repair at replication block 5.work with Bloom helicase - reduce frequency of crossover Two major pw to release the replication block; 1. TLS -- using TLS polymerase, synthesis directly across the DNA damage 2. HR -- transient template switch from the damage to newly synthesized daughter strands There has been proposed that db holliday junctions are dissolved by concerted action of RecQ helicase, Blm and Topo-IIIalpha R...

Note: Mutant cells defective in DNA repair pathways provide a sensitive high-throughput assay for genotoxicity DNA repair during replication (S-phase) 1. TLS 2. HR 3. FA DNA repair throughout cell cycle; 1. base excision 2. nucleotide excision 3. NHEJ In this paper, the panel that they used; 1. DNA damage checkpoint - ATM 2. HR - Rad54, XRCC3, and UBC13 3. NHEJ - Ku70 4. ICL - FANCC 5. TLS - Rev3 6. NER - XPA and XPG 7. BER - DNA pol-beta My understanding in this paper - they relied on one particular lesion will be majorly used by one particular pw (how much fold should be different then bc DNA repair has the redundancy?). Good points for DT40 again (in year 2010) -  1.High targeted integration 2.Stable karyotype/phenotype even for the long subculture 3.Short doubling time Still, it is chicken - some genes could not be conducted though DNA repair pws have been said to be conserved throughout evolution. 1. Genetic manipulation in mammalian cells - diffi...

Note for: Characterization of environmental chemicals with potential for DNA damage using isogenic DNA repair-deficient chicken DT40 cell lines (doi: 10.1002/em.20656) US Tox21 program -- evaluate the detection of genotoxic cpds. This study focused on cytotoxicity by using DT40 with deficient in DNA repair pathway. Using 7-isogenic DNA repair-deficient pw cell line to identify the types of DNA damage. Criteria to judge; 1.clastogenicity (ability to break the DNA) in mutant and WT 2.ability to induce gH2Ax positive foci by melphalan 3.72-hr viability through the liquid assay 4.using more DNA repair deficient cell lines to clearly identify the damage induced 5.involvement of ROS in induction of DNA damage At the end, it proposed that DT40 and theirs DNA-repaired deficient lines are useful tool to detect 1.genotoxic cmp. 2.identify the nature of DNA damage of the challenges 3.analyzing mechanism of mutagenesis Rational; Because of the number of chemica...

Note: RAD18 and Poly(ADP-Ribose) Polymerase Independently Suppress the Access of Nonhomologous End Joining to Double-Strand Breaks and Facilitate Homologous Recombination-Mediated Repair (doi: 10.1128/mcb.01243-06) Rad18 in yeast involves in post-replication repair but not dsb repair. Show less sensitivity toward cpt when generating ko. In contrast, Rad18 ko in dt40 showed high sensitivity toward cpt and involve in hr to repair dsb. The authors mentioned that when deleting another key factor of nhej in hr deficient cell, and thus restoring the activity of hr, this mean that that hr factor (Rad18) plays role in the balancing between hr and nhej. At stalled replication fork, Rad18 and Parp1 are used to control the balance between hr and nhej, by which the suppress the nhej to prevent toxic nhej during replication folk collapse. PRR - there are two pws, 1.translesion, 2.template switch via HR Translesion using the specialized polymerase to bypass the damage. Rad6 and Rad18 ...

Note: Differential usage of non-homologous end-joining and homologous recombination in double strand break repair (doi: 10.1016/j.dnarep.2006.05.022 ) they mentioned that HR play dominant role in yeast, however, NHEJ contributes to DSB repair in vertebrates (my guess is that higher vertebrate genome is more complex, NHEJ is much easier to solve DSB very quick). There is the tight regulation on the switching HR and NHEJ -- events that determine the cell to go for either HR or NHEJ is cell cycle phase and DSB nature. DSB is lethal damage, if there is one unrepaired DSB, it can induce apoptosis. For the cycling cell, DSB occurs mainly during the replication. For the ionizing radiation -- i can generate break at any stages, or even the "packed chromatin" -- therefore, during the G2 and G1 which the chromosomes are packed -- it will be hard to find the homology in G2 (from sister-chromatid which is "packed") and the homology in G1 (from homology se...

Note: Genetic dissection of vertebrate 53BP1: A major role in non-homologous end joining of DNA double strand breaks (doi: http://dx.doi.org/10.1016/j.dnarep.2006.03.008 ) mutation of 53BP1 in mammalian causing 1.cellular sensitivity toward radiation. 2.defect in checkpoint But DT40-53BP1(-/-) 1.intra-S phase checkpoint was normal 2.G2-M checkpoint was normal once there is the DSB -- 53BP1 is the earliest protein to recruit and form foci. In mammalian, defect in 53BP1 causes the cell cycle delays after the damage. The sequence of NHEJ; 1. Ku70/80 2.DNA-PK --> phosphorylate Artemis nuclease Artemis in IR break fixing is required more studies. Late S-G2; HR and NHEJ play role in "IR-induced" double strand break G1-early S; NHEJ is dominant AA from 203-1716 was removed. Sensitivity toward irradiation with asynchronously growing 53BP1-/- -->biphasic pattern. 53BP1(-/-) also increased the rate of HR --> this mean th...