Random Records

It is very old paper though - Note for: Reduced X-Ray Resistance and Homologous Recombination Frequencies in a RAD54 (-/-) Mutant of the Chicken DT40 Cell Line (doi: 10.1016/S0092-8674(00)80198-1 ) Done in S. cerevisiae before and want to investigate in vertebrate -- therefore, DT40 is chosen. 1. Rad54(-/-) was generated 2. Testing this KO - found out that sensitive to radiation, Ig gene conversion reduce, lower targeted integration 3. Complementary testing with human cDNA -- regain radio-resistant and targeted integration **first report on DBS in vertebrate cells. In yeast model study --> found out that either Rad51,Rad52 and Rad54 mutants --> DSB stay long after injure by X-ray Targeted integration in mammal is hard due to the majority of DSB repair occurs through NHEJ (my guess would be less S-phase period and no check point during intra-S? --> need to check which mammalian cell lines were used) Vertebrate cell line model: DT40 is a good mode...

Note for: The DNA-damage response in human biology and disease (doi: 10.1038/nature08467) DNA damage response detection is very essential process in living organism to maintain the right balance between the diversity (fit well to the external) and the disease (unfit to the external). 1.DNA lesion can occur either both physiological and pathological condition. 2.physilogical lesion -- DNA mismatch//break by topo-i and topo-ii Damage occurs through: 1.oxidative respiration 2.redox-cycling (membrane of mitochondria) 3.Fenton reaction (redox reaction catalyzed by Fe) 4.NOS and ROS produce during inflammation and infection DNA double-strand break is rarely found but very toxic once it is generated. DNA damage responses differentially occur depending on the classes of DNA lesions. The process could be separated as follow; 1.damage or stalled replication/transcription 2.detection by sensors 3.recruitment of mediators 4.amplifying the signal 5.transduc...

Note for: Molecular Role of RNF43 in Canonical and Noncanonical Wnt Signaling (doi: 10.1128/MCB.00159-15) It is a bit hard to follow when reading this paper. Wnt1 class-- canonical Wnt go through beta-catenin Degradation complex includes; 1.adenomatous polyposis coli (APC) 2.axin 3.casein kinase Ialpha (CKIalpha) 4.glycogen synthase kinase 3beta (GSK-3beta) No Wnt-stimulant --> beta catenin is phosphorylated by degradation cpx leading to degradation by ubiquitin proteasome system by interact through SCFbetaTrCP ubiquitin ligase Finalized Wnt-catenin activation --> produce c-Myc which maintains undifferentiated state of cells. Wnt5a class-- non-canonical Wnt 1.not cause accumulation of beta-catenin and no induction of target genes 2.involve in cell polarity and cell migration+antagonizes Wnt/beta-catenin -- play role as tumor suppressor RNF43 suppresses both canonical and non-canonical but in different manner -- The research quest...

Paper: Genetics of Opisthorchis viverrini-related cholangiocarcinoma (doi: 10.1097/MOG.0000000000000162) Aim: Looking at the genetic, epigenetic, and transcriptional landscape of CCA Method; whole exome sequencing and target sequencing Finding; CCA-related genes mutations TP53 KRAS SMAD4 novel CCA-related genes mutations chromatin remodeling BAP1 ARID1A MLL3 IDH1/2 Wnt-signaling RNF43 PEG3 KRAS/G-protein GNAS ROBO2 OV and non-OV related; Set of gene mutations  are different which may link to different pathogenesis of CCA Adult Ov can stay at the biliary tract and remain in host for 10 years Important risk factor for CCA; Chronic inflammation in biliary tract epithelia Epigenetic changes for Ov-related; Hypermethylation of hMLH1 promoter (44.6%) -- reduced expression  and function (to me no surprised why it affect the RNF43 mutations -- due to RNF43 has the microsatellite in the coding region whi...

Paper: Ring finger protein 43 expression is associated with genetic alteration status and poor prognosis among patients with intrahepatic cholangiocarcinoma (doi: 10.1016/j.humpath.2015.12.027) Marks -- P < .05, considered statistically significant (even for Kaplan-Meier analysis) Abstract; RNF43-- 1.central maintenance of genome integrity 2.cellular homeostasis Ring finger ligases -- involve in malignancy RNF43 -- frequently mutated in many type of malignancy (ICC is part of this malignancy) Gap; Expression level of RNF43 in ICC never been observed Purposed; 1.Investigate expression level in ICC 2.Identify RNF43 polymorphisms in ICC tissues 3.Observe correlation between RNF43 expression vs RNF43 mutation/polymorphisms, clinicopathological features and prognosis Finding; 1.RNF43 low correlated with rs2257205 and RNF43-somatic mutations 2.down reg of RNF43 (both protein and mRNA level) related to overall survival poor (meaning RNF43 could play role as tumor suppressor) 3...

Human genome; 1. ~3,000*10^6 bases (just remember that it is around 1 CD capacity - 3-4GB) 2. ~20,000 Protein coding genes 3. ~1% of genome --Protein coding exons human SNP; bases change in every 1000 bases therefore, human SNPs (3000*10^6)/1000 = 3 millions (3*10^6) Genome different within the species (except twins) 99.9% identical PS.There is a group of people interested in the same thing; http://book.bionumbers.org/ https://bionumbers.hms.harvard.edu/search.aspx -- Prefix for number Ref: https://en.wikipedia.org/wiki/Metric_prefix

At a glimpse. In each package will be used for specific type of analysis. For my case, I am interested in the data from GeoDataset which in the gene expression data deposited on NCBI. Also the ggplot that can represent data in the graphical ways. One thing that I notice about myself is that I totally forget some functions/definitions in mathematics, I have not used some definitions for a while ago and got shocked during the training. Some definitions are used for turning some values to make the calculation go through the pipeline, for example, complex number. It will be a steep learning curve for sure, the commands will be new to me but the pipeline or thinking-step to get the output should be the same and can be applied to any computer programming. PS. I have provided information for the self-study in the useful links --- Additional - before I forget, each window in R has a different function (pic below); Window 1\\ script writing-> use for writing the scri...