The C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy

Ik‑Young Choi,Eun‑Chae Kwon,Nam‑Soo Kim 한국유전학회 2020 Genes & Genomics Vol.42 No.7

Background The apparent disconnection between biological complexity and both genome size (C-value) and gene number (G-value) is one of the long-standing biological puzzles. Gene-dense genomic sequences in prokaryotes or simple eukaryotes are highly constrained during selection, whereas gene-sparse genomic sequences in higher eukaryotes have low selection constraints. This review discusses the correlations of the C-value and G-value with genome architecture, polyploidy, repeatomes, introns, cell economy and phenomes. Discussion Eukaryotic chromosomes carry an assortment of various repeated DNA sequences (repeatomes). Expansion of copies of repeatomes together with polyploidization or whole-genome duplication (WGD) are major players in genome size (C-value) bloating, but genomes are equipped with counterbalancing systems such as diploidization, illegitimate recombination, and nonhomologous end joining (NHEJ) after double-strand breaks (DSBs). The lack of these efficient purging systems allowed the accumulation of repeat DNA, which resulted in extremely large genomes in several species. However, the correlation between chromosome number and genome size is not clear due to inconsistent results with different sets of species. Positive correlations between genome size and intron size and density were reported in early studies, but these proposals were refuted by the results with increased numbers of species, in which genome-wide features of introns (size, density, gene contents, repeats) were weakly associated with genome size. The assumption of the correlations between C-value and gene number (G-value) and organismal complexity is acceptable in general, but this assumption is often violated in specific lineages or species, suggesting C- and G-value paradoxes. The C-value paradox is partly explained by noncoding repeatomes. The G-value paradox can also be explained by several genomic features: (1) one gene can produce many mature mRNAs by alternative splicing, and eukaryotic gene expression is highly regulated at both the transcriptional and translational levels; (2) many proteins exert multiple functions during development; (3) gene expansion/contraction are frequent events in the gene family among evolutionarily close species; and (4) sets of homeotic genes regulate development such that organismal complexity is sometimes not clear among organisms. A large genome must be burdensome in terms of cell economy, such that a large genome constraint results in the distribution of genome sizes skewed to small genomes. Moreover, the C-value can affect the phenome. A strong positive correlation has been recognized between genome size and cell size, but the relationship is weak or null with higher-level traits. Additional analyses of the relationship between the C-value and phenome should be carried out, because natural selection acts on the phenotype rather than the genotype. Conclusions Dramatic advancement in genomics has given some answers to the C-value and G-value paradoxes. We know the mechanisms by which the current genomes have been constructed. However, basic questions have not yet been fully resolved. Why have some species retained small genomes yet some closely related species have large genomes? Random genetic drift and mutational pressure might have affected for genome size in the limited population size during evolution; thus, genome size may be quasiadaptable rather than the best adaptive trait.

직업적 연폭로가 일부 신경행동학적 검사수행에 미치는 영향

안익수,안현철,김용배,리갑수,김화성,황규윤,최은,장봉기,이성수,안규동,이병국 순천향대학교 산업의학연구소 1999 순천향산업의학 Vol.5 No.1

In order to investigate that blood lead levels of lead exposed workers is associated with decreased performance in neurobehavioral tests in adults, we investigate 78 workers in a battery industry. Three items among neurobehavioral core test battery of World Health Organization, including digit span, Santa ana dexterity, digit symbol were administered to workers occupationally lead exposed workers by operational guide for the WHO neurobehavioral core test battery. Blood lead (PbB) and zinc protoporphyrin in whole blood (ZZP) were selected as an index of lead exposure. Detailed occupational history such as exposed agent, age, work duration, smoking and drinking habits, were recorded as confounding factors. After controlling age, the results of digit span and digit symbol among the neurobehavioral tests were significant contributed by PbB.

철학(哲學) : 우암(尤庵) 송시열(宋時烈)의 직철학(直哲學)과 교육문화

김익수 ( Ik Soo Kim ) 한국사상문화학회 2008 韓國思想과 文化 Vol.42 No.-

우암 송시열(1607~1689)은 理學은 율곡이이(李珥 1536~1584)에게서 전수했으나 直哲學은 스승인 金長生(1548~1631)으로부터 전수(傳受)받았는데 조선조에서 直의 哲學은 송익필(1534~1599)로부터 비롯된 것이다. 우암은 孔子, 孟子, 程子, 朱子, 靜庵, 退溪, 栗谷 등의 사상을 貫通할 수 있는 直哲學 하나(一)로 義理之學을 세웠으니 ``大人之學``이라고 칭할만하다. 조선시대의 학문은 性理學이지만 시대를 초월하여 古今이 通貫되는 것이 直哲學이며 교육문화이므로 원천적으로 孔子易學의 直哲學으로 소급해서 연구되어야 한다. 우암의 直哲學은 平生의 生活哲學이었지만 모든 인류를 바르고 곧고(正直) 淸明하고 光明하게 문화민족으로 살아갈 수 있는 교육문화가 꽃필 修養論이기에 時·空을 초월한 永續性을 갖는다. 朱子를 尊信하고 朱子學에 전심한 우암의 春秋大一統思想의 義理는 민족의 주체성과 국가관이 확고하며 나아가서는 平天下, 곧 世界人類 平和思想임이 확실하다. 현대의 우리나라는 정치와 교육이 일치(政·敎一致)되지 않고 있어서 민족의 주체가 확고하지 않고 윤리가 지극히 문란하며 교육의 본연을 잃고 있다. 國史의 正體性이 허약하고 도덕이 부실(不實)한 토대위의 경제건설은 미래지향적이 아니다. 이런 때에 우암의 直哲學과 교육문화로 시대의 철학과 교육문화로 정착하여 世界化할 때 세계속에 우리나라가 도덕종주국으로 찬란한 교육문화가 인류평화사상으로 꽃필 가능성이 높다고 전망한다. 21세기는 문화의 세기라고 한다. 우암의 直哲學의 修養論은 현대 교육문화철학으로서 가치가 절대적이라고 판단되므로 새로운 정립이 시급하다. Uam Song Si-yeol(1607-1689) inherited the study of li from Yulgok Yi I(1536-584) while he succeeded the tradition of the philosophy of Righteousness from his teacher Kim Jang-saeng(1548-1631). The tradition of the philosophy of the Righteousness began with Song Ik-pil(1534-1599) at the early period of Joseon Dynasty. Uam would be considered as a ``Great Man in Neo-Confucianism because he established the philosophy of Righteousness that provide the theory unifying the cores of the teachings of Confucius, Mencius, Ch`engcius, Chu His, Jeongam, Toegye, and Yulgok. The major trend of the scholarly tradition of Joseon was Neo-Confucianism, however, this timeless philosophy of Righteousness is the core as well as the education. That is why Confucius study of Righteousness needs to be the first step to understand the Neo-Confucian tradition of Joseon. Uam`s philosophy of Righteousness was the philosophy of his life itself. At the same time, he emphasized the education to cultivate the all humankind to live with righteousness and wise to live as civilized men. From this his idea of education receives the respect regardless the time and space. Uam`s righteousness from his philosophy of the Great Union of Spring and Autumn, which reflects his dedication and respect for the Chu His is the one to set up sound national and racial self-esteems to achieve the peaceful co-existence of the mankind. There is a gap between politics and education in Korea today and it causes the collapse of education with the lack of identity and moral. Economic development cannot be futuristic when it lacks the identity in national history and collapse of moral standard. This is why the Uam`s philosophy of Righteousness and civilized education need to be reestablished and internationalized to promote the possibility of Korea becomes a leader of world moral and education. Since twenty-first century is the era of culture, Uam`s thoughts and the concept of education has an unchallengeable values.

연작업자들에서의 δ -aminolevulinic acid dehydratase 유전형질의 다형성이 신기능에 미치는 영향

안익수,황보영,김용배,리갑수,이성수,장봉기,함정오,안규동,이병국 순천향대학교 산업의학연구소 2001 순천향산업의학 Vol.7 No.1

δ-aminolevulinic acid hehydratase (ALAD) is a polymorphic enzyme that has two alleles, ALAD1 (ALAD1-1 as phenotype) and ALAD2 (ALAD1-2 or ALAD2-2 as phenotype). ALAD genotype has been reported to modify the toxicokinetics of lead. To investigate the influence of ALAD genotype polymorphism on renal function in lead workers, author studied 1022 male lead workers and 149 non lead workers in the same industries. For the cross-sectional renal function indices, blood urea nitrogen (BUN), serum creatinine, uric acid and total protein were selected. Blood lead and blood zinc protoporphyrin were also measured as indices of lead exposure. Information on weight, age, job duration, smoking & drinking history were collected. Following results are as follows: 1. Whereas the mean (standard deviation) of blood lead and blood ZPP of lead workers were 27.2±12.5 ㎍/㎗ and 57.7±37.8 ㎍/㎗, those of non-lead workers in the same premises were 14.9±6.5 ㎍/㎗ and 44.6± 15.8 ㎍/㎗ respectively. The difference of mean blood lead and blood ZPP between two groups were statistically significant. 2. Whereas the prevalence of the variant allele, ALAD2 in 1022 lead workers was 10.2 %, the prevalence of that in 149 non-lead workers was 7.4 %. But there was no difference of prevalence between two groups. 3. The mean±standard deviation of blood lead of subjects with ALAD1 was 25.5± 12.7 ㎍/㎗ and was slightly lower than that of subjects with ALAD2 (26.5±10.9 ㎍/㎗), and the mean±standard deviation of blood ZPP of subjects with ALAD1 was slightly higher than that of subjects with ALAD2 (56.7±37.3 ㎍/㎗ vs 48.9±18.6 ㎍/㎗). But the differences of blood lead and blood ZPP between two genotypes were not statistically significant. 4. There were no differences of cross-sectional renal function indices (BUN, serum creatinine, uric acid and total protein) either by lead workers and non-lead workers or two genotypes. 5. In multiple regression analysis of ALAD genotype on BUN after controlling for possible confounders (sex, weight, job duration, smoking and drinking status), the mean of BUN in ALAD2 subjects was 0.629 ㎎/㎗ lower than ALAD1 subjects with a weak statistical significance (p=0.07). But in logistic analysis of ALAD genotype on median value of BUN revcaled that subjects of ALAD2 genotype were 32% less likely to have median value or more of BUN than subjects of ALAD1 with odd ratio of 0.618 (95% confidence interval 0.411-0.920). 6. In multiple regression analysis of ALAD genotype on serum creatinine after controlling for possible confounders (sex, weight, job duration, smoking and drinking status), the mean of serum creatinine in ALAD2 subjects was 0.0271 ㎎/㎗ lower than ALAD1 subjects with statistical significance (p=0.02). On the other hand, in logistic analysis of ALAD genotype on median value of serum creatinine revealed that subjects of ALAD2 genotype were 30% less likely to have median value or more of scrum creatinine than subjects of ALAD1 with odd ratio of 0.700 (95% confidence interval 0.442-1.080). With the above results, it was found that the variant allcle, ALAD2 appeared to modify the association of lead and renal function and ALAD2 genotype may be supportive for the protective effect of lead.

주파수확산통신을 위한 카오스 PN 시퀀스의 특성

이익수,여지환 대구대학교 과학기술연구소 1999 科學技術硏究 Vol.5 No.5

The existing random numbers or PN sequences are secure and reproducible with a implementation of digital circuit. But it is hard to change random sequences that is due to limit period size and digital system realization. This work proposes the chaotic PN sequence(CPNS) of analog and binary types which is coded by the chaotic sequence, that can be extracted from a 3-dimensional discrete time chaotic generation equation(3D²CGE) for generating various chaotic signals. A CPNS method using 3D²CGE has several advantage: the generation is easy, and various families with arbitrary size and sequence period can be obtained because the chaotic systems has parameters. Furthermore, we have tested a correlation function and the degree of statistical independence of each CPNS that is evaluated in order to apply to spread spectrum communication. Experimental results show that the proposed CPNS codes are used for the spreading sequence and secure communication codes.

외상성 대장 및 직장 손상

김익용,김상희,윤광수,김히욱 대한대장항문학회 1997 Annals of Coloproctolgy Vol.13 No.3

韓國産 검정망둑(Tridentiger)屬 魚類의 分類學的 硏究

金益秀,崔允 全北大學校 基礎科學硏究所 1991 基礎科學 Vol.14 No.1

1982年부터 1987年 사이에 우리나라 沿岸과 汽水 및 淡水에서 採集한 Tridentiger屬 魚類의 標本을 檢討하여 이들을 새로운 檢索表와 함께 再記載하고 本 調査에서 처음으로 밝혀진 1未記錄種에 대해 記載하였다. 즉 韓國産 Tridentiger屬에는 T. trigonocephalus, T. obscurus, T. nudicervicus, T. brevispinis가 出現하는 것이 確認되었다. T. trigonocephalus는 동해안과 남해안의 沿岸과 汽水域에 廣範圍하게 分布하였고 T. nudicervicus는 전북 옥구군 미성읍과 금강河口에서만 出現하였다. 形態的으로 T. obscurus와 아주 類似하여 그동안 우리나라에서 T. obscurus와 同一種으로 여겨졌던 T. brevispinis는 논산, 부안, 삼척(담수), 아산, 영덕 등의 淡水에서 出現하였고, T. obscurus는 제주도 (서귀포, 중문), 삼척(맹방해수욕장 부근), 보길도 등의 汽水에서 出現하였다. 또한 T. brevispinis는 體長에 대한 百分比로서 제1등지느러미 제3기조의 길이가 암컷은 14.4-24.7, 수컷은 16.1-32.0이고, 새파수가 8-11인 반면, T. obscurus는 體長에 대한 百分比로서 제1등지느러미 제3기조 길이가 암컷은 15.4-33.0, 수컷은 24.4-43.8 이고 새파수가 11-14개라는 점에서 2種은 잘 區分되었다. The goby genus Tridentiger of Korea is reviewed and keys to following four species of the genus Tridentiger are provided for T. trigonocephalus, T. obscurus, T. nudicervicus and T. brevispinis. Among them, T. brevispinis is reported for the first time from Korea with the descriptions and illustrations of other three species of this genus in this paper. The external features of T. brevispinis are very similar with those of T. obscurus, however T. brevispinis is distinguished from T. obscurus by having the shorter 3rd dorsal spine, lesser number of gill rakers and longer intestine length. T. obscurus lives in the river mouth and esturaies around the coast of Korea, while T. brevispinis is collected from only the fresh water area.

한국산 송사리 두 종의 교잡실험

김익수,김소영 全北大學校 基礎科學硏究所 1994 基礎科學 Vol.16 No.-

지리적으로 분리 분포하고 있는 한국산 송사리 두 집단간의 분류학적 위치를 검토하기 위하여 두 집단간의 형태 및 교잡실험을 하여 비교하고 그 자손에 대하여 핵형과 발생율을 비교 조사하였다. 이들 두 종의 대부분의 계수 계측형질은 대체로 유사하지만 가슴지느러미 기조수, 뒷지느러미의 기조수 및 척추골 수에 있어서 차이를 보였다. 가슴지느러미 기조수의 경우 Oryzias latipes는 9∼10의 범위를 갖는데 비해 O. sinensis는 8∼9개 이었고 뒷지느러미 기조수에 있어서는 O. latipes는 19∼21의 범위를 보인 반면 O. sinensis는 17∼19개 이었다. 또한 척추골 수에 있어서도 O. latipes가 31∼33개인 반면 O. sinensis는 30∼31개 이었다. 2n 염색체가 48인 O. latipes와 46인 O. sinensis 두 종간의 교잡에 의한 제 1세대의 염색체 수는 2n이 47로 하나의 large metacentric chromosome을 가지고 있었다. 그리고 이들 제 1세대를 자가교배하여 얻은 제 2세대의 염색체 수는 2n=46,47,48개 이었는데 이들의 비율은 13:3:1로 나타났다. 또한 두 종의 교잡에 의한 제1세대의 수정율 및 부화율은 동일 종간의 교잡의 결과와 큰 차이가 없는데 비해 제1세대를 자가교배하여 얻은 제2세대의 경우에는 수정율, 부화율에서 감소를 보였고 기형인 개체가 대조군에 비해 증가했다. 이러한 결과들로 보아 이들 두 종은 지리적 분리요인에 의하여 염색체가 분화되었다고 보아 이 두 집단은 분류학적으로 아종이라기 보다는 종으로 간주하는 것이 타당하다고 생각한다. Cytogenetic studies and hybridization experiment using two populations of Oryzias latipes from Korea were conducted in order to examine their systematic positions. In the chromosome number of specimens examined. O. sinensis had 46 with a pair of large metacentrics and O. latipes had 48 chromosomes without a pair of lage metacentrics. However, the diploid chromosome number of the hybrid between O. latipes and O. sinensis was 47 and they had a large metarcentric chromosome in their karyotype. In the F_2 hybrids, distribution of chromosome number was variable among individuals. Hatching rates showed little difference between control and hybrids. However, hatchiabilties of F_2 hybrids were decreased by 83.3% as compared with F_1 offspring. Incidence of abnormal larvae was increased by increaed by 15.3% as compared with their parents. These results indicate that the two karyotype populations formerly regarded as two subspecies would be two distinct allopatric sibling species O. sinensis and O. latipes.

미꾸리과 어류 남방종개 Iksookimia hugowolfeldi (Cobitidae)의 핵형

김익수,최은경,양현,고명훈 한국어류학회 2003 韓國魚類學會誌 Vol.15 No.2

영산강의 상류인 전라남도 장성군 북하면 신계리에서 2003년 2월 3월에 채집된 남방종개 Iksookimia hugowolfeldi 암컷 14마리와 수컷 9마리의 신장 조직에서 염색체를 조사하였다. 2n 염색체수는 50개이었는데 핵형은 meta-submetacentrics이 24개이고, subtelo-telocentrics가 26개였으며 FN은 74개이었다. 염색체에서 배수체나 암수간의 성적이형은 보이지 않았다. Chromosome analysis of the southern spined loach, Iksookimia hugowolfeldi was investigated in 23 individuals collected at Bukha-myon, Jangseong-gun, Jeollanam-do Provice, Korea an upper stream of the Yongsan River, in February, 2003. The diploid modal number of the specimens examined was 50, and the karyotype was composed of 24 metacentrics-submetacentrics and 26 subtelocentrics-telocentrics. Polyploidy and sex dimorphism were not observed in the present species.

잡종기원의 Cobitis sinensis-longicorpus comples(Pisces, Cobitidae)에 대한 생식소의 조직학적 연구

김익수,박종영 全北大學校 基礎科學硏究所 1994 基礎科學 Vol.16 No.-

낙동강 상류에서 서식하는 기름종개 Cobitis sinensis와 왕종개 C.longicorpus 사이의 잡종에서 유래된 집단이라고 생각되는 C. sinensis-longicorpus complex의 생식소에 대하여 조사하였다. 이들 집단은 조사시간 중 272개체가 채집되었는데 그 가운데 암컷이 266개체로 거의 대부분을 차지하였고 수컷은 오직 6개체만 발견되었다. 암컷의 난소조직은 정상적인 발달단계를 보이는 생식 능력있는 난소였다. 그러나 수컷의 정소는 testicular lobule에 텅 빈 vacuole 구조가 많이 포함된 조직에 정원세포나 정모세포는 있지만 정세포와 정자가 생기지 않는 점으로 보아 생식능력이 없는 비정상적인 정소라고 생각한다. 이와같은 결과는 C. sinensis-longicorpus complex의 암컷 집단이 유연종들의 수컷의 도움으로 생식이 유지되는 독특한 체계를 지니고 있음을 시사해 주고 있다. Cobitis sinensis-longicorpus complex considered as hybrid origin between C. sinensis and C. longicorpus coccurred ommonly in the upper streams of the Nakdong River, Korea. Histological examinations of their gonad were accompanid with 272 individuals of C. sinensis-longicorpus complex collected. Most of fishes collcted were females, however, only 6 individuals were found males. The ovarian tissues of females are completely fertile undergoing normal oogenensis. In the male gonads, testicular lobule structure with abnormal vacuolar tissues were observed. Spermatogonia and spermatocytes were also observed of their testis however spermatids or sperms were not shown in their developmental stages. From these facts, we infer that female population of C. sinensis-longicorpus complex may be unique reproductive hierarchy accomplishing their reproduction with participation of males of their closely related bisexual species.