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Genome Analysis of the Domestic Dog (Korean Jindo) by Massively Parallel Sequencing
Kim, Ryong Nam,Kim, Dae-Soo,Choi, Sang-Haeng,Yoon, Byoung-Ha,Kang, Aram,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Jong-Joo,Ha, Ji-Hong,Toyoda, Atsushi,Fujiyama, Asao,Kim, Aeri,Kim, Min-Young,Park, Kun-Hyan Oxford University Press 2012 DNA research Vol.19 No.3
<P>Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the <I>TCOF1</I> locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.</P>
Novel mechanism of conjoined gene formation in the human genome.
Kim, Ryong Nam,Kim, Aeri,Choi, Sang-Haeng,Kim, Dae-Soo,Nam, Seong-Hyeuk,Kim, Dae-Won,Kim, Dong-Wook,Kang, Aram,Kim, Min-Young,Park, Kun-Hyang,Yoon, Byoung-Ha,Lee, Kang Seon,Park, Hong-Seog Springer 2012 Functional & integrative genomics Vol.12 No.1
<P>Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene. This result led us to propose a novel mechanism of CG formation: the complete removal of the poly(A) signal site from the upstream parent gene is a prerequisite for the CG transcriptional machinery to continue transcribing uninterrupted into the intergenic region and downstream parent gene. The removal of the poly(A) signal sequence from the upstream gene region appears to be caused by a deletion or truncation mutation in the human genome rather than post-transcriptional trans-splicing events. With respect to the characteristics of CG sequence structures, we found that intergenic regions are hot spots for novel exon creation during CGTV formation and that exons farther from the intergenic regions are more highly conserved in the CGTVs. Interestingly, many novel exons newly created within the intergenic and intragenic regions originated from transposable element sequences. Additionally, the CGTVs showed tumor tissue-biased expression. In conclusion, our study provides novel insights into the CG formation mechanism and expands the present concepts of the genetic structural landscape, gene regulation, and gene formation mechanisms in the human genome.</P>
Childhood Sexual Abuse and Cortical Thinning in Adults With Major Depressive Disorder
Jinyi Kim(Jinyi Kim),Chanju Lee(Chanju Lee),Youbin Kang(Youbin Kang),Wooyoung Kang(Wooyoung Kang),Aram Kim(Aram Kim),Woo-Suk Tae(Woo-Suk Tae),Byung-Joo Ham(Byung-Joo Ham),Jisoon Chang(Jisoon Chang),Ky 대한신경정신의학회 2023 PSYCHIATRY INVESTIGATION Vol.20 No.3
Objective A growing body of evidence reports on the effect of different types of childhood abuse on the structural and functional architecture of the brain. In the present study, we aimed to investigate the differences in cortical thickness according to specific types of childhood abuse between patients with major depressive disorder (MDD) and healthy controls (HCs). Methods A total of 61 patients with MDD and 98 HCs were included in this study. All participants underwent T1-weighted magnetic resonance imaging, and the occurrence of childhood abuse was assessed using the Childhood Trauma Questionnaire. We investigated the association between whole-brain cortical thickness and exposure to any type of childhood abuse and specific type of childhood abuse in the total sample using the FreeSurfer software. Results No significant difference was reported in the cortical thickness between the MDD and HC groups nor between the “any abuse” and “no abuse” groups. Compared to no exposure to childhood sexual abuse (CSA), exposure to CSA was significantly associated with cortical thinning in the left rostral middle frontal gyrus (p=0.00020), left (p=0.00240), right fusiform gyri (p=0.00599), and right supramarginal gyrus (p=0.00679). Conclusion Exposure to CSA may lead to cortical thinning of the dorsolateral prefrontal cortex, which is deeply involved in emotion regulation, to a greater extent than other types of childhood abuse.
Major chimpanzee-specific structural changes in sperm development-associated genes
Kim, Ryong Nam,Kim, Dae-Won,Choi, Sang-Haeng,Chae, Sung-Hwa,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Aeri,Kang, Aram,Park, Kun-Hyang,Lee, Yong Seok,Hirai, Momoki,Suzuki, Yutaka,Sugano, Sumio,Hashimoto, Ka Springer-Verlag 2011 Functional & integrative genomics Vol.11 No.3
2022 Clinical practice guidelines for central precocious puberty of Korean children and adolescents
Kim Su Jin,Kim Ji Hyun,Hong Yong Hee,Chung In Hyuk,Lee Eun Byoul,Kang Eungu,Kim Jinsup,Yang Aram,Rhie Young-Jun,Yoo Eun-Gyong,Shin Young-Lim,Choi Jin Ho,Kim Soo Young,Lee Ji Eun 대한소아내분비학회 2023 Annals of Pediatirc Endocrinology & Metabolism Vol.28 No.3
The Committee of Central Precocious Puberty of Korean Pediatrics and Adolescents of the Korean Society of Pediatric Endocrinology has newly developed evidence-based 2022 clinical practice guidelines for central precocious puberty in Korean children and adolescents. These guidelines provide the grade of recommendations, which includes both the strength of recommendations and the level of evidence. In the absence of sufficient evidence, recommendations are based on expert opinion. These guidelines have been revised and supplement the previous guidelines "Clinical Guidelines for Precocious Puberty 2011," and are drawn from a comprehensive review of the latest domestic and international research and the grade of recommendation appropriate to the domestic situation. This review summarizes the newly revised guidelines into 8 key questions and 27 recommendations and consists of 4 sections: screening, diagnosis, treatment, and long-term outcome of central precocious puberty.
Kim, Dae-Won,Kang, Aram,Choi, Sang-Haeng,Kim, Zang Geun,Kim, Woo-Jin,Kim, Hyung-Cheol,Park, Hong-Seog The Genetics Society of Japan 2009 Genes & genetic systems Vol.84 No.2
<P>We report here that a novel 1,869 bp repetitive sequence identified from the false killer whale (<I>Pseudorca crassidens</I>) could be a new molecular phylogenetic marker in cetaceans. Results of PCR amplification and southern blot hybridization using 16 species’ genomic DNAs from five different families revealed that the repetitive sequence is highly conserved within all Delphinidae species. Notably, specific primers designed for this repetitive sequence effectively amplified the targeted repetitive units, which were critically dependent upon the genetic phylogenies in the members of the Delphinidae cetaceans. Therefore, the novel sequences can be used as a useful phylogenetic marker for understanding the molecular evolutional studies in members of the Delphinidae family of cetaceans.</P>
이아람 ( Aram Lee ),최경호 ( Kyungho Choi ),김해중 ( Hai-Joong Kim ),이정재 ( Jeong Jae Lee ),최규연 ( Gyuyeon Choi ),김성주 ( Sungjoo Kim ),김수영 ( Su Young Kim ),조금준 ( Geumjoon Cho ),김영돈 ( Youg Don Kim ),서은숙 ( Eunsook 한국산업보건학회 2018 한국산업보건학회지 Vol.28 No.3
Objectives: This study aims to analyze manganese (Mn) concentrations in maternal and cord bloods at delivery and to estimate the Mn exposure risk for fetuses whose mothers were occupationally exposed to Mn. Materials and Methods: Forty-six pairs of maternal and cord blood samples were collected at delivery from mothers who were occupationally unexposed to Mn. Mn concentrations of blood were analyzed by graphite furnace atomic absorption spectrometer. Mn exposure levels for fetuses of female workers were estimated by simulating two working exposure scenarios. Results: The geometric mean concentration of Mn in maternal and cord blood were 27.0(1.34) ㎍/L, 46.6(1.25) ㎍/L, respectively. Transfer ratios of Mn from maternal to cord blood were 1.81±0.62, which indicated that the Mn concentrations in cord blood were higher than those in maternal blood. Mn concentrations in cord blood for the worse or general scenarios were estimated to 22.3-1,881 ㎍/L and 1.59-308 ㎍/L, respectively. The probabilities of exceeding 74 ㎍/L, which was adopted as a reference level reported in a previous study, were 95% and 44% for the two scenarios, respectively. Conclusions: Comparable levels of Mn exposure in maternal or cord blood to those in this study have shown various health effects in previous studies. This suggests that Mn exposure levels in mothers and fetuese in Korea need to be monitored and managed. In addition, female workers who are occupationally exposed to Mn should be protected from the exposure since their fetuses can be exposed to Mn at risky levels during their pregnancy.
“웬만하면 걷지”: 노인을 위한 보행자용 길 찾기 서비스 제안
김아람(Aram Kim),김혜미(Hyemi Kim),백한나(Hannah Baek),임서현(Seohyun Lim),홍성진(Sungjin Hong),김진우(Jinwoo Kim) 한국HCI학회 2016 한국HCI학회 학술대회 Vol.2016 No.1
본 연구는 정보사회의 불평등으로 정보 소외 현상을 겪는 노인의 정보격차 해소와 정보 활용 수준을 높이고자 노인을 위한 보행자용 길 찾기 서비스를 제안하고자 하였다. 노인의 전반적인 보행 경험요소를 도출하기 위해 Field Study 를 수행하여 총 14 개의 경험요소를 도출하고, 노인의 사용경험 제고를 위한 To-do 리스트와 함께 후속 연구에 대한 제언을 제공하였다. In this paper, we suggest guidelines to help develop pedestrian navigation specialized for elder citizens. By conducting a field study, we found Fourteen constructs from the elders’ everyday walking experiences based on their pedestrian navigations. From these constructs, we propose a to-do list to improve the elders’ user experiences for the navigation and provide a new question to explore further.