• Title/Summary/Keyword: comparative genomic hybridization

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Caulobacter ginsengisoli sp. nov., a Novel Stalked Bacterium Isolated from Ginseng Cultivating Soil

  • Liu, Qing-Mei;Ten, Leonid N.;Im, Wan-Taek;Lee, Sung-Taik;Yoon, Min-Ho
    • Journal of Microbiology and Biotechnology
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    • v.20 no.1
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    • pp.15-20
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    • 2010
  • A Gram negative, aerobic, nonspore-forming, straight or curved rod-shaped bacterium, designated Gsoil $317^T$, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized using a polyphasic approach. Cells were dimorphic, with stalk (or prostheca) and nonmotile or nonstalked and motile, by means of a single polar flagellum. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil $317^T$ was most closely related to Caulobacter mirabilis LMG $24261^T$ (97.2%), Caulobacter fusiformis ATCC $15257^T$ (97.1 %), Caulobacter segnis LMG $17158^T$ (97.0%), Caulobacter vibrioides DSM $9893^T$ (96.8%), and Caulobacter henricii ATCC $15253^T$ (96.7%). The sequence similarities to any other recognized species within Alphaproteobacteria were less than 96.0%. The detection of Q-10 as the major respiratory quinone and a fatty acid profile with summed feature 7 ($C_{18:1}\;{\omega}7c$ and/or $C_{18:1}\;{\omega}9t$ and/or $C_{18:1}\;{\omega}12t;$ 56.6%) and $C_{16:0}$ (15.9%) as the major fatty acids supported the affiliation of strain Gsoil $317^T$ to the genus Caulobacter. The G+C content of the genomic DNA was 65.5 mol%. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain Gsoil $317^T$ and its closest phylogenetic neighbors were below 11%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $317^T$ should be classified as representing a novel species in the genus Caulobacter, for which the name Caulobacter ginsengisoli sp. novo is proposed. The type strain is Gsoil $317^T$ (=KCTC $12788^T=DSM\;18695^T$).

A healthy delivery of twins by assisted reproduction followed by preimplantation genetic screening in a woman with X-linked dominant incontinentia pigmenti

  • Kim, Myung Joo;Lyu, Sang Woo;Seok, Hyun Ha;Park, Ji Eun;Shim, Sung Han;Yoon, Tae Ki
    • Clinical and Experimental Reproductive Medicine
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    • v.41 no.4
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    • pp.168-173
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    • 2014
  • The purpose of this study is to report a successful twin pregnancy and delivery in a female patient with X-linked dominant incontinentia pigmenti (IP) who underwent assisted reproductive technology followed by preimplantation genetic screening (PGS). A 29-year-old female with IP had a previous history of recurrent spontaneous abortion. A molecular analysis revealed the patient had a de novo mutation, 1308_1309insCCCCTTG(p.Ala438ProfsTer26), in the inhibitor of the kappa B kinase gamma gene located in the Xq28 region. IVF/ICSI and PGS was performed, in which male embryos were sexed using array-based comparative genomic hybridization (aCGH). After IVF/ICSI and PGS using aCGH on seven embryos, two euploid male blastocysts were transferred with a 50% probability of a viable male pregnancy. The dizygotic twin pregnancy was confirmed and the amniocentesis results of each twin were normal with regard to the mutation found in the mother. The patient delivered healthy twin babies during the 37th week of gestation. This case shows the beneficial role of PGS in achieving a successful pregnancy through euploid male embryo gender selection in a woman with X-linked dominant IP with a history of multiple male miscarriages.

CAMVS(V1.0) : CGH Analyzer and Map Viewer using S-Plus(V1.0)

  • Kim, Sang-Cheol;Park, Chan-Hee;Seo, Min-Young;Jeong, Ha-Jin;Kim, In-Young;Chung, Hyun-Cheol;Rha, Sun-Young
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • 2004.11a
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    • pp.131-137
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    • 2004
  • DNA 단계에서의 유전자의 증폭과 소실은 종양의 발생과 진행에 중요한 역할을 한다. 유전자의 변화를 관찰하기 위해서 Comparative Genomic Hybridization(CGH) 기술이 많이 이용되어져 왔다. 최근에는 이러한 CGH 기술을 응용하여 cDNA microarray 를 이용한 고밀도 CGH(Microarray-CGH) 기술이 보고 되고 있다. Microarray-CGH 에서 유전자별 변화 정도를 유전자의 log-비의 값의 변화 정도와 염색체 위치 정보를 이용하여 DNA 단계에서의 유전자의 변화 정도를 확인 할 수 있다. 또한 동일한 유전자의 칩을 사용하여 RNA단계에서의 발현 양상과 직접 비교할 수 있는 장점이 있다. 현재 microarray 분석법은 많이 개발되고 실용화 되고 있으나 Microarray-CGH 분석을 위한 프로그램들은 아직 초보 단계며, 생물학자들이 사용하기 힘들고, 프로그램에 분석 자료를 적용하기 어려운 경향이 있다. 위와 같은 단점을 보완하기 위해서 개발된 CAMVS(V1.0) 프로그램은 S-plus(2000)을 기반으로 개발하였고, 복잡한 분석보다는 모든 결과들을 이미지화 할 수 있으며 파일로 결과를 쉽게 확인할 수 있도록 디자인하였다. CAMVS(V1.0)는 전체 염색체를 각 실험별로 비교 분석하는 부분, 특정 염색체를 특정 실험별로 비교 분석하는 부분과 실험간의 차이를 통계적으로 비교 분석하는 3 가지 카테고리로 구성되어 있다. 쉬운 알고리즘과 사용의 편리함, 분석결과의 다양한 그래픽, 새로운 알고리즘 추가의 용이성 등이 CAMVS(V1.0)가 가지고 있는 장점이며, Microarray-CGH를 분석하는데 아주 유용한 분석 도구이다.

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Replication of the Association between Copy Number Variation on 8p23.1 and Autism by Using ASD-specific BAC Array

  • Woo, Jung-Hoon;Yang, Song-Ju;Yim, Seon-Hee;Hu, Hae-Jin;Shin, Myung-Ju;Oh, Eun-Hee;Kang, Hyun-Woong;Park, Seon-Yang;Chung, Yeun-Jun
    • Genomics & Informatics
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    • v.8 no.1
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    • pp.19-27
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    • 2010
  • To discover genetic markers for autism spectrum disorder (ASD), we previously applied genome-wide BAC array comparative genomic hybridization (array-CGH) to 28 autistic patients and 62 normal controls in Korean population, and identified that chromosomal losses on 8p23.1 and on 17p11.2 are significantly associated with autism. In this study, we developed an 8.5K ASD-specific BAC array covering 27 previously reported ASD-associated CNV loci including ours and examined whether the associations would be replicated in 8 ASD patient cell lines of four different ethnic groups and 10 Korean normal controls. As a result, a CNV-loss on 8p23.1 was found to be significantly more frequent in patients regardless of ethnicity (p<0.0001). This CNV region contains two coding genes, DEFA1 and DEFA3, which are members of DEFENSIN gene family. Two other CNVs on 17p11.2 and Xp22.31 were also distributed differently between ASDs and controls, but not significant (p=0.069 and 0.092, respectively). All the other loci did not show significant association. When these evidences are considered, the association between ASD and CNV of DEFENSIN gene seems worthy of further exploration to elucidate the pathogenesis of ASD. Validation studies with a larger sample size will be required to verify its biological implication.

Interstitial deletion of 5q33.3q35.1 in a boy with severe mental retardation

  • Lee, Jin Hwan;Kim, Hyo Jeong;Yoon, Jung Min;Cheon, Eun Jung;Lim, Jae Woo;Ko, Kyong Og;Lee, Gyung Min
    • Clinical and Experimental Pediatrics
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    • v.59 no.sup1
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    • pp.19-24
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    • 2016
  • Constitutional interstitial deletions of the long arm of chromosome 5 (5q) are quite rare, and the corresponding phenotype is not yet clearly delineated. Severe mental retardation has been described in most patients who present 5q deletions. Specifically, the interstitial deletion of chromosome 5q33.3q35.1, an extremely rare chromosomal aberration, is characterized by mental retardation, developmental delay, and facial dysmorphism. Although the severity of mental retardation varies across cases, it is the most common feature described in patients who present the 5q33.3q35.1 deletion. Here, we report a case of a de novo deletion of 5q33.3q35.1, 46,XY,del(5)(q33.3q35.1) in an 11-year-old boy with mental retardation; to the best of our knowledge this is the first case in Korea to be reported. He was diagnosed with severe mental retardation, developmental delay, facial dysmorphisms, dental anomalies, and epilepsy. Chromosomal microarray analysis using the comparative genomic hybridization array method revealed a 16-Mb-long deletion of 5q33. 3q35.1(156,409,412-172,584,708)x1. Understanding this deletion may help draw a rough phenotypic map of 5q and correlate the phenotypes with specific chromosomal regions. The 5q33.3q35.1 deletion is a rare condition; however, accurate diagnosis of the associated mental retardation is important to ensure proper genetic counseling and to guide patients as part of long-term management.

A case of de novo duplication of 15q24-q26.3

  • Kim, Eun-Young;Kim, Yu-Kyong;Kim, Mi-Kyoung;Jung, Ji-Mi;Jeon, Ga-Won;Kim, Hye-Ran;Sin, Jong-Beom
    • Clinical and Experimental Pediatrics
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    • v.54 no.6
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    • pp.267-271
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    • 2011
  • Distal duplication, or trisomy 15q, is an extremely rare chromosomal disorder characterized by prenatal and postnatal overgrowth, mental retardation, and craniofacial malformations. Additional abnormalities typically include an unusually short neck, malformations of the fingers and toes, scoliosis and skeletal malformations, genital abnormalities, particularly in affected males, and, in some cases, cardiac defects. The range and severity of symptoms and physical findings may vary from case to case, depending upon the length and location of the duplicated portion of chromosome 15q. Most reported cases of duplication of the long arm of chromosome 15 frequently have more than one segmental imbalance resulting from unbalanced translocations involving chromosome 15 and deletions in another chromosome, as well as other structural chromosomal abnormalities. We report a female newborn with a de novo duplication, 15q24- q26.3, showing intrauterine overgrowth, a narrow asymmetric face with down-slanting palpebral fissures, a large, prominent nose, and micrognathia, arachnodactyly, camptodactyly, congenital heart disease, hydronephrosis, and hydroureter. Chromosomal analysis showed a 46,XX,inv(9)(p12q13),dup(15)(q24q26.3). Array comparative genomic hybridization analysis revealed a gain of 42 clones on 15q24-q26.3. This case represents the only reported patient with a de novo 15q24-q26.3 duplication that did not result from an unbalanced translocation and did not have a concomitant monosomic component in Korea.

A case of Sotos syndrome presented with end-stage renal disease due to the posterior urethral valve

  • Cho, Won Im;Ko, Jung Min;Kang, Hee Gyung;Ha, Il-Soo;Cheong, Hae Il
    • Journal of Genetic Medicine
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    • v.11 no.2
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    • pp.74-78
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    • 2014
  • Sotos syndrome (SS, OMIM 117550) is characterized by prenatal and postnatal overgrowth with multiple congenital anomalies. However, there have been few cases of growth retardation caused by renal failure from infancy. We report a case of dysplasia of the bilateral kidneys with renal failure and poor postnatal growth. A 2-month-old boy visited the emergency room owing to poor oral intake and abdominal distension. He was born at the gestational age of 38 weeks with a birth weight of 4,180 g. After birth, he had feeding difficulty and abdominal distension. Upon physical examination, his height and weight were in less than the 3rd percentile, while his head circumference was in the 50th percentile on the growth curve. He also showed a broad and protruding forehead and high hairline. Blood laboratory tests showed severe azotemia; emergent hemodialysis was needed. Abdominal ultrasonography revealed bilateral renal dysplasia with multiple cysts and diffuse bladder wall thickening. A posterior urethral valve was suggested based on vesicoureterography and abdominal magnetic resonance findings. Results of a colon study to rule out congenital megacolon did not reveal any specific findings. The conventional karyotype of the patient was 46, XY. Array comparative genomic hybridization study revealed a chromosome 5q35 microdeletion including the NSD1 gene, based on which SS was diagnosed. We describe a case of SS presenting with end stage renal disease due to posterior urethral valve. The typical somatic overgrowth of SS in the postnatal period was not observed due to chronic renal failure that started in the neonatal period.

UNDERSTANDING OF EPIGENETICS AND DNA METHYLATION (인간 게놈의 Copy Number Variation과 유전자 질환)

  • Oh, Jung-Hwan;Nishimura, Ichiro
    • Maxillofacial Plastic and Reconstructive Surgery
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    • v.30 no.2
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    • pp.205-212
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    • 2008
  • Genetic variation in the human genome occurs on various levels; from the single nucleotide polymorphism to large, microscopically visible chromosome anomalies. It can be present in many forms, including variable number of tandem repeat (VNTRs; e.g., mini- and microsatellites), presence/absence of transposable elements (e.g., Alu elements), single nucleotide polymorphisms, and structural alterations (e.g., copy number variation, segmental duplication, inversion, translocation). Until recently SNPs were thought to be the main source of genetic and phenotypic human variation. However, the use of methods such as array comparative genomic hybridization (array CGH) and fluorescence in situ hybridization (FISH) have revealed the presence of copy number variations(CNVs) ranging from kilobases (kb) to megabases (Mb) in the human genome. There is great interest in the possibility that CNVs playa role in the etiology of common disease such as HIV-1/AIDS, diabetes, autoimmune disease, heart disease and cancer. The discovery of widespread copy number variation in human provides insights into genetic variability among populations and provides a foundation for studies of the contribution of CNVs to evolution and disease.

A refined Panax ginseng karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs

  • Waminal, Nomar Espinosa;Choi, Hong-Il;Kim, Nam-Hoon;Jang, Woojong;Lee, Junki;Park, Jee Young;Kim, Hyun Hee;Yang, Tae-Jin
    • Journal of Ginseng Research
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    • v.41 no.4
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    • pp.469-476
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    • 2017
  • Background: Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion: Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.

Bacillus ginsengihumi sp. nov., a Novel Species Isolated from Soil of a Ginseng Field in Pocheon Province, South Korea

  • Ten Leonid N.;Im Wan-Taek;Baek Sang-Hoon;Lee, Jung-Sook;Oh, Hee-Mock;Lee, Sung-Taik
    • Journal of Microbiology and Biotechnology
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    • v.16 no.10
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    • pp.1554-1560
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    • 2006
  • A Gram-positive, aerobic or facultative anaerobic, non motile, endospore-forming bacterial strain, designated Gsoil $114^T$, was isolated from a soil sample of a ginseng field in Pocheon Province (South Korea), and was characterized taxonomically by using a polyphasic approach. It grew well on nutrient agar medium and utilized a limited number of organic substrates as sole carbon sources, including D-xylose and some other carbohydrates, but did not utilize L-amino acids and organic acids. The isolate was positive for oxidase test but negative for catalase, and negative for degradation of macromolecules such as starch, cellulose, xylan, casein, chitin, and DNA. The G+C content of the genomic DNA was 41.8 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major fatty acids were $anteiso-C_{15:0}$ (32.1%), $iso-C_{15:0}$ (30.5%), and $anteiso-C_{17:0}$ (30.2%). Comparative 16S rRNA gene sequence analysis showed that strain Gsoil $114^T$ fell within the radiation of the cluster comprising Bacillus species and joined Bacillus shackletonii LMG $18435^T$ with a bootstrap value of 95%. The highest 16S rRNA gene sequence similarities were found with Bacillus shackletonii LMG $18435^T$ (97.6%), Bacillus acidicola DSM $14745^T$ (96.9%), Bacillus sporothermodurans DSM $10599^T$ (96.5%), and Bacillus oleronius DSM $9356^T$ (96.5%). The phylogenetic distance from any other validly described species within the genus Bacillus was less than 96%. DNA-DNA hybridization experiments showed that the DNA-similarities between strain Gsoil $114^T$ and closest phylogenetic neighbors were less than 39%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $114^T$ (=KCTC $13944^T$=DSMZ $18134^T$) was classified in the genus Bacillus as the type strain of a novel species, for which the name Bacillus ginsengihumi sp. nov. is proposed.