Heui-Soo Kim

A comparison of TSPY genes from Y-chromosomal DNA of the great apes and humans: sequence, evolution, and phylogeny.

The genes for testis-specific protein Y (TSPY) were sequenced from chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), orangutan (Pongo pygmaeus), and baboon (Papio hamadryas). The sequences were compared with each other and with the published human sequence. Substitutions were detected at 144 of the 755 nucleotide positions compared. In overviewing five sequences, one deletion in human, four successive nucleotide insertions in orangutan, and seven deletions/insertions in baboon sequence were noted. The present sequences differed from that of human by 1.9% (chimpanzee), 4.0% (gorilla), 8.2% (orangutan), and 16.8% (baboon), respectively. The phylogenetic tree constructed by the neighbor-joining method suggests that human and chimpanzee are more closely related to each other than either of them is to gorilla, and this result is also supported by maximum likelihood and strict consensus maximum parsimony trees. The number of nucleotide substitutions per site between human and chimpanzee, gorilla, and orangutan for TSPY intron were 0.024, 0.048, and 0.094, respectively. The rates of nucleotide substitutions per site per year were higher in the TSPY intron than in the TSPY exon, and higher in the TSPY intron than in the ZFY (Zinc Finger Y) intron in human and apes.

Effects of HERV-R env Knockdown in Combination with Ionizing Radiation on Apoptosis-Related Gene Expression in A549 Lung Cancer Cells

Radiotherapy has played a key role in the management of non–small-cell lung cancer (NSCLC). However, the use of radiotherapy in treating NSCLC is limited because of the intrinsic radiation resistance of tumor cells and injury to adjacent normal tissues. Many oncogenes are reported to be involved in radioresistance. Thus, novel moleculartargeting approaches to enhance the radiosensitivity of NSCLC cells are required to improve the therapeutic efficiency of radiotherapy. In this study, we report that expression of the human endogenous retrovirus-R (HERV-R) env gene is greatly elevated in γ-irradiation resistant A549 cells compared with radiation sensitive H460 cells. In addition, the HERV-R env gene was significantly increased in A549 cells after treatment with γ-irradiation. HERV-R env knockdown by siRNA in irradiated A549 cells led to overexpression of TP53 mRNA, followed by significant elevation in the levels of CDKN1A mRNA. Moreover, the expression of the apoptosis-related FAS-1 gene was increased, whereas the expression levels of the anti-apoptotic gene BCL2 were significantly decreased in the A549 cells in which the HERV-R env was suppressed by γ-irradiation. These results suggest that knockdown of HERV-R env with γ-irradiation causes cell cycle disturbances, which in turn induces apoptosis. In conclusion, the combination of HERV-R env knockdown and γ-irradiation has the potential to improve the therapeutic efficiency of radiotherapy for NSCLC.

Major histocompatibility complex DQA1 nucleotide sequences of gelada baboon (Theropithecus gelada), olive baboon (Papio anubis), and yellow baboon (Papio cynocephalus)

Non-human primates provide valuable models to investigate the causes of human diseases, to test candidate vaccines against infectious pathogens, and to evaluate the efficacy of fertility regulating agents. Understanding the characteristics of the primate major histocompatibility complex (MHC) may be critical in the interpretation of results of vaccine trials and investigations of possible associations between MHC and disease. Routine typing of primate MHC alleles has been hampered by the unavailability of specific immunological reagents and allele-specific oligonucleotide probes. Hence, there is a need to generate adequate nucleotide sequence information that can be used to design polymerase chain reaction (PCR)based techniques for the typing of primate MHC alleles. Among the primates, MHC-DQA1 of gorilla, chimpanzee, and rhesus macaques have been well characterized (Christ et al. 1994; Sauermann et al. 1995; Slierendregt et al. 1993; Kenter et al. 1993; Bontrop et al. 1995). In the present study, genomic DNA was isolated from ten baboons(Papio anubisN = 5,Papio cynocephalus N = 2, Theropithecus gelada N = 2, Papio hamadryasN = 1) and the polymorphic second exon of the DQA1 locus was amplified using GH26 and GH27 PCR primers (Scharf et

Nucleotide sequences of the major histocompatibility complex DQA1 locus of Cercopithecus monkeys

Major histocompatibility complex (MHC) gene products are highly polymorphic. This characteristic contributes to antigen binding repertoire and thus plays a vital role in the generation of effective immune responses to a variety of infectious pathogens (Bontrop et al. 1996; Parham and Ohta 1996). The nucleotide sequence diversity of the polymorphic MHC class II genes is located in the second exon and encodes amino acid residues that are found in the antigen binding site (Slierendregt et al. 1993). Previous studies have shown that most Old World monkeys lack MHC-DQA2andDQB2 (Bontrop et al. 1995; Kenter et al. 1992). In contrast, primate DQA1 is polymorphic and some allelic lineages are shared by humans, apes, and monkeys (Bontrop et al. 1995; Sauermann et al. 1995; Christ et al. 1994). In the present study, we analyzed the DQA1 locus of twenty-two AfricanCercopithecusmonkeys maintained at the Institute of Primate Research, Nairobi, Kenya. These primates included three African green monkeys (C. aethiops),seventeen Sykes monkeys (C. mitis)representing the three Kenyan subspecies, including five highland sykes (C. m. kolbi),seven lowland sykes (C. m. albogularis) , five blue sykes(C. m. stuhlmanni) , and two De-Brazza’s monkeys(C. neglectus ). In addition, two black-and-white colobus monkeys(Colobus guereza) and one black mangabey (Cercocebus aterrimus) were analyzed. Genomic DNA was isolated from peripheral blood lymphocytes and the DQA1 gene region was amplified using GH26 and GH27 polymerase chain reaction (PCR) primers (Scharf et al. 1986). The PCR products (242 or 239-bp) were cloned using the TA cloning kit (Invitrogen, San Diego, CA) and nucleotide sequences determined using an automated DSQ-1 sequencer (Shimadzu, Japan) and cycle sequencing reagents (Perkin-Elmer, Branchburg, NJ). For each individual, sequences were determined from at least two PCR amplifications and a minimum of three plasmid clones. Computerassisted analysis of the obtained nucleotide sequences was performed to compare similarity between individuals of the same and different species and also with published human and primate sequences using DNA database (DDBJ) FASTA (version 1.30). The designation of the genes represented in these sequences has been standardized according to the recommendation contained in an earlier proposal (Klein et al. 1990). An alignment of representative sequences from each species is shown in Fig. 1. In some instances, the sequences derived from different individuals were identical ( 499%) and one representative was used in the alignment. The results of this study provide additional sequence information on fifteen new MHC-DQA1alleles of African Old World monkeys and extends the previous compilation of non-human primate DQA1sequences (Bontrop 1994). The nucleotide sequence data reported in this paper have been submitted to the EMBL/GeneBank databases and have been asigned the following accession numbers: D88582 (African green monkey, VER 1548), D88583 (African green monkey, VER 1621), D88739 (African green monkey, GRIV 14), D88675 (blue sykes, BLU 26), D88676 (blue sykes, BLU 29), D88677 (Blue sykes, BLU 28), D89536 (blue sykes, BLU 30), D89537 BLU 31), D88678 (highland sykes, SYK 269), D88679 (highland sykes, SYK 276), D88680 (highland sykes, SYK 354), D89531 (highland sykes, SYK 191), D89532 (highland sykes, SYK 314), D88681 (lowland sykes monkey, SYL 51), D88682 (lowland sykes monkey, SYL 70), D88683 (lowland sykes monkey, SYL 66), D88684 (lowland sykes monkey, SYL 120), D889534 (lowland sykes, SYL 73), D89534 (lowland sykes, SYL 1 19), D89535 (lowland sykes, SYL 117), D88580 (De Brazza’s monkey, DEB 53), D88581 (De Brazza’s monkey, DEB 54), D88579 (black mangabey, BLM 29) and D88578 (black and white colobus monkey, COL 38), and D89530 (black and white colobus monkey, COL 32)

Molecular Analysis of Alternative Transcripts of CCDC94 Gene in the Brain Tissues of Rhesus Monkey

The genome of the rhesus monkey has diverged as an average sequence identity of ~93%. The rhesus monkey has been widely used as a non-human primate in the field of biomedical and evolutional research. Insertion of transposable elements (TEs) induced several events such as transcriptional diversity and different expression in host genes. In this study, 112 transcripts were identified from a full-length cDNA library of brain tissues of the rhesus monkey. One transcript (R54) showed a different expression pattern between human and rhesus monkey tissues. This phenomenon can be an explanation that R54 transcript was acquired by splicing a donor site derived from exonization of the L2A element. Therefore, integration of TEs during primate radiation could contribute to transcriptional diversity and gene regulation.

Establishment of Genetic Characteristics and Individual Identification System Using Microsatellite Loci in Jeju Native Horse

This study was conducted to establish the individual identification system and to estimate the genetic characteristic of Jeju native horse (JNH) using 13 microsatellite markers located on different horse autosomes. The markers were genotyped on 191 animals from five horse breeds including Jeju native horse (JNH). In total, 138 alleles were detected from the genotypes of 13 microsatellite markers. The average heterozygosities ranged from 0.317 to 0.902 and the polymorphic information content (PIC) ranged from 0.498 to 0.799 in JNH. We found that there were significant differences in allele frequencies in JNH when compared with other horse breeds. In ATH4 marker, there were specific allele frequence pattern that some of allele only found in JNH, Mongolian horse (MONG) and Jeju racing horse (JRH). The calculated cumulative power of discrimination (CPD) was 99.9% when nine microsatellite loci were used for analysis in the individual identification system. Also, the matching probability that two unrelated animals would show the same genotypes, was estimated to be . Therefore, in the nine markers used in this study can be used for individual identification in the Jeju native horse population.

Bioinformatics Analysis of Gene Expression Regulation by Transposable Elements in Dementia Patients

Dementia is a progressive disease of increasing the dysfunction of intellectual and physical ability. In the aging society, many families are suffering from the caring the patients who are diagnosed with dementia. However, dementia is a complex disease affected by the genetic and environmental agents. In the present study, we investigated the transposable elements in relation to dementia. From the analysis of dementia EST (expressed sequence tag) sequences, we found dementia candidate genes, and analyzed expression profiles and repeat elements using bioinformatics tools. This analysis showed that 98 genes were affected in their mRNA sequences by transposable elements expression. Their expressions were affected by the integration of different transposable elements (SINE, LINE, LTR, DNA) during the primate evolution. We believe that our work will be of significant interest to genome scientists, and may help them gain insight into implication of transposable elements expression in dementia.

Identification and phylogenetic analysis of the human endogenous retrovirus HERV-W pol in cDNA library of human fetal brain

A human endogenous retroviral family (HERV-W) has recently been described that is related to multiple sclerosis-associated retrovirus (MSRV) sequences that have been identified in particles recovered from monocyte cultures from patients with multiple sclerosis. Two pol fragments (HWP-FB10 and HWP-FBl2) of HERV-W family were identified and analysed by the PCR approach with cDNA library of human fetal brain. They showed 89 percent nucleotide sequence similarity with that of the HERV-W (accession no. AF009668). Deletion/insertion or point mutation in the coding region of the pol fragments from human fetal brain resulted in amino acid frameshift that induced a mutated protein. Phylogenetic analysis of the HERV-W family from GenBank database indicates that the HWP-FB10 is very closely related to the AC000064 derived from human chromosome 7q21-q22. Further studies on the genetic relationship with neighbouring genes and functional role of these new HERV-W pol sequences are indicated.