Soonwan Kim

1. Paper review on Transcriptomics<ppt>:

https://drive.google.com/file/d/1Jrap7KyrfS-1X7Fv44ZqP1rGBdMTgS4F/view?usp=sharing

2. Inheritance of Acquired adaptive Characters (IAC)

 https://drive.google.com/file/d/1l7_lD9bc5rsSOHafjovPCkntTliAEKWV/view?usp=sharing

3.Report Genomic View on aging

https://drive.google.com/file/d/14MUlWejOZR3jW-YOw2501_w8C6G4QSXz/view?usp=sharing

4.Report om Epigenomics: Principles and challenges of genome-wide DNA methylation analysis

https://drive.google.com/file/d/1QbyxnEVI3N4v0o2IwPvmO17D5i37uU3g/view?usp=sharing

5.Type2_Diabetes_and GWAS<ppt>

https://drive.google.com/file/d/1dbtvtFmcW5xlQZNa7rUpTaUnEDgTQtmq/view?usp=sharing

 

A. Terms related to Genomics

1) Contig- is an abstract term which is used to define the long nucleotide sequence that was derived overlapping many short sequences.The longer contig, the better quality of DNA sequencing.

2) Scaffold- is made by overlapping several contigs. 

3) SNP- single nucleotide polymorphism is a variation of single nucleotides in certain regions of genomes. Usually, genome of a every individual has certain sequences which are highly conserved. SNP is used to determine the paternity.

4) Whole genome shotgun sequencing- is one way of sequencing genome. Its main principle is that it repeatedly and randomly sequesters short nucleotide sequences. By doing so, researchers obtain a huge data which is processed by computer programs to produce final product, whole genome sequence.

5) YAC - Yeast artificial chromosome is a vector used for transfer of DNA molecules. YAC is built by yeast centromere and telomere. There are two other vector types, but this one possesses the highest capacity.

6) Accession number- is a special number or code which has its unique target (item). Nowadays, biological field is overwhelmed by data and it becomes difficult to find your subject. That's why accession number can facilitate the access to the certain object. 

7) Genetic diversity- refers to the diversity of genetic components of the genome such as variety of genes, alleles, SNPs and etc. Genetic diversoty gives an opportunity to adapt fir external changes and to evolve. There are different ways to measure the genetic diversity, but each of them is adapted for certain case. Common criteria to measure diversity is heterozygosity and richness per allele. 

8) Heterozygosity- demonstrates genetical heterogeneity. It means how many different versions of the same locus are present in genome. Usually, inbreeding causes low heterozygosity i.e. low diversity in genome.

9) Penetrance- is a proportion of individuals in the population which expresses the feature of interest. 

10) Genomics- is a big data study of interaction between genomic components. Cell viability is mediated not only by gene-gene interaction, but also cis and trans regulatory sequences. 

11) Epigenetics- is a study of inheritence by non-genomical methods such as by RNA, mithochondrial genome, proteins and histones. 

12) Orthology- is the relationship between homologous sequences originated from the same ancestor but in different species. When a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous

13) Paralogy- is the relationship between homologous sequences originated from the same ancestor in the same species. Paralogous genes arise as a result of duplication rather than speciation.

14) Imprinting- is a phenomenon in which the penetrance and expressivity of genes depend on the parent that carried the gene.

15) BLAST- is a method for aligning different sequences, compare them and calculating the similarity between different sequences. It gives us the insight about how two sequences are similar to each other. There are many types of sequence alignment depending on the nature of sequences and goal of the process.

16) RT-PCR- Reverse Transcription-PCR is often used for determining the expression level of certain genes or for constructing cDNA library. This method implies reverse transcriptase which synthesizes DNA strand based on mRNA sequence. This DNA is called complementary DNA and its characteristic property is lack of introns. 

17) CRISPR- is a new method for generation of site-specific mutation. It utilizes two main components: Cas9, protein with two domains, and guideRNA. Last one is responsible for selection of target and cas9 is responsible for degrading target, itself. This mechanism was first found in bacterial cells and was defined to be a immunal defense process against viruses. 

18) Artificial selection- as opposed to natural selection this process selects organisms that are beneficial for human beings . This process occurs unnaturally and organisms survive and thrive according to human's will. During the last 10000 years humans domesticated lots of animals and plants. Most of them show significant change in their lifestyles. 

19) Natural selection- is a theory that explains the mechanims of evolution. According to it organisms survive if they are well fitted to their environment. This fit can be interpreted in different ways; different species use different strategies to transmit their genetic information to the next generation.

20) Phylogeography- is an interdiscipline study of geographical evolution of species. This science studies how ancient species evolved and dispersed around the world.

21) Bioinformatics- is an interdiscipline science which implies IT techniques to study biological phenomena. This is highly demanded field which can process and analyze huge volumes of information, facilitating the science process. Without it, there would be know "-omics" sciences and we couldn't sequence whole human genome. 

22) DNA-Protein crosslinks- or DPCs, are structures that connect genomic DNA with various types of proteins including histones, TFs and etc. These structures have been discovered recently and currently they are studied by Natalia Tretyakova (IBS CGI 3rd Symposium) DPCs accumulate in heart and brain tissues with age. 

23) Pleiotropy- is a phenomenon of influence a single gene to many features of organisms. Usually, every gene has its own "target audience" and mutation of the gene will cause problems only in the corresponding "audience". However, in pleiotropy one gene affects multiple audiences. 

24) Pseudogene- is a sequence of DNA similar to a gene but nonfunctional; probably the remnant of a once-functional gene that accumulated mutations.

25) Repetitive DNA- is a sequences of varying lengths that occur in multiple copies in the genome; it represents much of the human genome

26) FISH- is a method of visualizing chromosomes in metaphase/anaphase stages. The main property of FISH is that it is sequence specific technique i.e. it binds binds only if its RNA constituent finds complementary sequence in chomosome molecule. RNA contains some fluorescent properties by which we can visualize our target.

27) STRUCTURE- is a software. It is based oon clustering method and it utilizes Markov chain model and Bayesian approach. It is used to determine phylogeographical structure of the species. 

28) Fertile Crescent- is a land in ancient times where agriculture and then domestication of cats occured. This place is located somewhere in Mediterraen territory. 

29) Allelic richness- demonstrate the average number of alleles per locus. Decrease in allelic richness can be interpreted as the reduction in the population's potential to adapt to different circumstances. Genetic diversity is important because it allows to adapt to sudden and unexpected situations. That's why, many ~ecologists worry about purebred animals.