20240722_184857

Allele : the different forms of a gene
- Homozygous : having two copies of the same allele (e.g. SS, ss)
- Heterozygous : having two different alleles of the gene (e.g. Ss)
Genome : the totality of all the genes (e.g. HMGA2)
chromatin : a fibrous complex, 여러 neucleosome 이 합진 것
Nucleosome: DNA + 8 Histones
chromosome : the long, thin threads, 여러 chromatin 이 뭉진 것, 평소 안 존재하다가 세포분열때만 나타남.
chromatid : one-half of a replicated chromosome
locus : a particular site on a chromosome
mutation : the alterations of genome, changes of neucleotide sequence of DNA
- wild type : one particular allele that is present in most individuals in nature, giving rise to an expected phenotype/trait
phenotype : the physical appearance of an organism
Seroprevalence: the frequency of individuals with antibody to a particular virus
mosaic, or mosaicism, involves the presence of two or more populations of cells with different genotypes in one individual
- quantification: The rate (%) of mosaicism (presence of three indels or more)
- affected by genetic background of the oocyte
- (Dussaud et al. 2018, PMID 30346378)

Figure 5: Relative copy number of integrated transgenes. Quantification of eGFP integration sites relative to CDX2 gene as described in protocol section. Box plot from 25^th to 75^th percentile. Dots represent the different transgenic embryos that were generated. The comparison of transgenes integrated sites between the two lentiviral constructs is significantly different (Unpaired parametric t-test, p = 0.001). Please click here to view a larger version of this figure.

Transgenes	Number of collected eggs	Number of injected eggs	Number of implanted eggs	Number of collected embryos	Number of embryos with transgene integration	Number of embryos expressing transgene
Lentiviral mediated transgenesis
CMV-eGFP	48	36	34	22	16	16
pCAG-eGFP	63	57	51	32	27	25
Neurog3-enh-eGFP	94	94	83	47	39	36
Chr6-eGFP	122	82	82	48	34	0
Pronuclear injection
Neurog3-enh-LacZ	1302	1234	542	263	38	3

Table 1: Step by step quantitative report during the complete procedure. During the course of the procedure, the total numbers of eggs or embryos were counted. The first column represents the total number of eggs that were retrieved from the oviducts of superovulated females. Only eggs with clear 2 polar bodies and/or visible pronuclei were injected and are reported. After injection and a few hours in culture only the injected eggs that were not lysed and had a normal morphology were implanted. Next the total number of embryos that were collected from the pseudopregnant females are counted. Finally, embryos that had integrated the transgene and expressed the reporter are listed in the last two columns. The same features are also given for comparison with an experiment using standard pronuclei DNA injection. Here the transgene contained the Neurog3 enhancer driving expression of a beta-galactosidase reporter gene (Neurog3-enh-LacZ). Please click here to download this file

Congenic: two organisms that differ in only one locus and a linked segment of chromosome are defined as congenic
- How to develop a congenic strain?: Congenic strains are generated in the laboratory by mating two inbred strains (usually rats or mice), and back-crossing the descendants 5–10 generations with one of the original strains, known as the recipient strain. Typically selection for either phenotype or genotype is performed prior to each back-cross generation. In this manner either an interesting phenotype, or a defined chromosomal region assayed by genotype, is passed from the donor strain onto an otherwise uniform recipient background. Congenic mice or rats can then be compared to the pure recipient strain to determine whether they are phenotypically different if selection was for a genotypic region, or to identify the critical genetic locus, if selection was for a phenotype.
genetic linkage : physically linked on the same chromosome (Mendelian law 를 따르지 않는),
- drosophia 에서 body color gene과 wing size gene이 같은 chromosome 에 위치 → 몰려서 유전되고, 발현할 가능성이 증가.
Plasmid : in bacteria, additional smaller, circular chromosomes, in aadtion to main chromosomes,
PCR : DNA 를 amplification 함. DNA polymerase 사용해서.
One gene, one polypeptice 원직 : 한 protein 에 여려개의 polypeptide 니까, 여러 gene 이 하나의 protein 을 code. 반대로 한 gene 이 여러 protein 을 code 할 수도 있음.
Transcript : Mrna of the gene
Codon : mRNA에서의, 3개의 neuclotide가 하나의 aa 를 endode하는 단위. 즉 이 세개의 조합으로 20여개의 aa 를 만들어냄.
Codon optimization
- Definition
  - 종간 발현을 하고자 할 때, 특정 생물제의 유전자를, host의 codon에 최적화시켜 주어야 하는데 이를 codon optimization이라 합니다.
- Purpose
  - ↑ expression, ↓ immunogenicity
- Background
  - 생물이 유전자에 사용하는 codon은 종마다 균주마다 다릅니다. 가령 알지닌은 6개의 코돈이 지정하는데 생물종마다 여섯개중에 한두개만 사용하지요.
  - 가령 사람유전자를 대장균에서 발현시키려면 사람유전자 알지닌코돈 중 대장균이 거의 사용하지 않는 코돈이 많다면 단백질합성이 알지닌에서 멈춰버립니다.
- Methods
  - 간단히 웹상의 프로그램으로 최적화를 할 수 있습니다. 아미노산 서열을 paste하여 넣고 run을 하면 해당 host에 적합한 DNA서열을 찾아주는 방식입니다.
  - http://www.encorbio.com/protocols/Codon.htm
  - 다음 site는 생물체들의 codon usage를 일목요연하게 정리해 놓은 곳입니다. http://www.kazusa.or.jp/codon/
  - 가령 H. pylori에서 어느 유전자를 발현시킨다고 봅시다. 유전자의 orf를 가져다가 DNASTAR 같은 프로그램을 사용하면 각 아미노산의 사용빈도를 알 수 있습니다. 발현숙주로 사용하는 대장균의 각 아미노산별 코돈 사용빈도는 아래의 사이트에서 조회할 수 있습니다. http://www.kazusa.or.jp/codon/
Transcription : RNA polymerase가 DNA의 promoter (a special sequence of DNA)에 강하게 결합하며 시작.
DNA내에 Intron (to be removed) & Exon 존재
Nucleic acid: When we string together the nucleotides A, T, C, and G to make DNA, we get something called a “nucleic acid”
Nucleic acid hybridization : probe (single stranded nucleic acid from another source) 를 원래의 DNA 의 한 strand 에 붙임.
Gene expression: We say that a gene is “expressed” when that gene is used to make RNA templates.
Restriction enzyme (=restriction endoneuclease) : DNA 를 부숨. (반대는 DNA ligase)
- → Gel electrophoresis로 DNA 들을 separate.
DNA fingerprinting : 친자 확인
- Single nucleotide polymorphisms (SNP) : point mutation 이용
- Short tandem repeats (STR) : Short repetitive DNA sequence that occur side by side on the chromosome
Genetic linkage : the co-inheritance of the genetic marker (i.e. the reference point) & the disease-causing allele.
RFLP (Restriction fragment length polymorphism) : point mutation 등이 있으면 restriction enzyme 에 의해 짤린후의 길이가 제각각
Epigenetics : changes in the expression of gene that occur without changing the DNA sequence, e.g. DNA methyation
Haplotype :
- Definition
  - a set of SNPs that are present on a segment of chromosome and usually inherited as a unit
  - haplotype은 하나의 염색체상에 통계적으로 연관된 SNP(Single Nucleotide Polymorphism) 집합이다.
  - 같은 chromosome 내에서 함께 유전되는 경향이 있는 인접한 SNP들의 집합을 말한다.
  - 함께 따라다니는 SNP 현상들의 집합인 Block을 SNP Haplotype이라 한다.
  - Similar to Linkage Disequilibrium
- EXAMple 1.
```
AT'''A'''GTCACG'''T'''ACGTAT'''T'''ACG
AT'''C'''GTCACG'''A'''ACGTAT'''G'''ACG
AT'''C'''GTCACG'''A'''ACGTAT'''G'''ACG
```
  이와 같은 경우 SNP의 집합은 3번째, 10번째, 17번째 위치의 것들이며, 3번째 위치에서는 A/C, 10번째 위치에서는 T/A, 17번째 위치에서는 T/G 의 SNP Type들이 관찰된 것이다. 그렇다면 이를 세 위치에서의 SNP들이 일어날 모든 경우의 수는 222 즉 다음과 같은 8가지 조합이 가능하다.
  ATT; ATG; AAT; AAG; CTT; CTG; CAT; CAG;
  이들 중 실제로 관찰된 결과는 ATT, CAG 단 2가지 뿐이다.
- Example

Table 1- The five most frequent haplotypes and GBA1 pathogenic variants.
Haplotype	Variants	5470G>A	4813G>A	Patients Frequency
H3	N370S	G	A	41/59 (69.0%)
H1	L444P	G	G	13/59 (22.0%)
H5	RecNcil	G	A	13/59 (22.0%)
H21	N370S	A	A	4/59 (6.8%)
H4	L444P	G	A	4/59 (6.8%)
* The percentage can be greater than 100%, as each patient can have up to two haplotypes.

의미
◆ 출처: https://arbcom.tistory.com/95 [데이콩풀]
Proteomics : proteome is the sum total of the proteins produced by an organism,
- Emergence :
  - a single gene can code for multiple proteins.

Uncertain Spans

“neucleosome”, “neucleotide”, “neuclotide”, “endode”, “polypeptice”, “원직”, “여려개의” — 한글 원문이 typo와 한국어식 영어 표기를 다수 포함. 그대로 전사.
“[데이콩풀]” — Proteomics 줄의 출처 링크 옆 한글 라벨. 시각적으로 ‘데이콩풀’ 처럼 보이며 OCR도 동일. 의미상 ‘데이’ 다음 글자가 모호하나 글자 그대로 전사.
“RecNcil” — Table 1 H5 행 ‘Variants’ 셀, ‘RecNcil’ 인지 ‘RecNciI’ 인지 모호. 시각적으로 ‘l’ 또는 ‘1’ 또는 ‘I’ 구분 어려움. ‘RecNcil’ 형태로 전사.
상단 ‘Speciation Event’ 다이어그램 — Organism 1, Organism 2 두 박스 안의 ‘Gene 1a’, ‘Gene 1b’ 라벨과 In-Paralog / Ortholog / Out-Paralog 연결 라벨만 보이며, 페이지 상단 제목 또는 figure caption은 photo 잘림으로 보이지 않음.

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