• 제목/요약/키워드: Flanking region

검색결과 182건 처리시간 0.027초

Single Nucleotide Polymorphisms linked to the SlMYB12 Gene that Controls Fruit Peel Color in Domesticated Tomatoes (Solanum lycopersicum L.)

  • Kim, Bichsaem;Kim, Nahui;Kang, Jumsoon;Choi, Youngwhan;Sim, Sung-Chur;Min, Sung Ran;Park, Younghoon
    • 원예과학기술지
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    • 제33권4호
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    • pp.566-574
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    • 2015
  • Yellow or transparent fruit peel color is caused by the accumulation or lack of naringenin chalcone (NG, C) in fruit peel and determines the red or pink appearance of tomato fruit, respectively. NGC biosynthesis is regulated by the SlMYB12 gene of the Y locus on chromosome 1, and DNA markers derived from SlMYB12 would be useful for marker-assisted selection (MAS) of tomato fruit color. To develop a gene-based marker, 4.9 kb of the SlMYB12 gene including a potential promoter region was sequenced from the red-fruited (YY) line 'FCR' and pink-fruited (yy) line 'FCP'. Sequence alignment of these SlMYB12 alleles revealed no sequence variations between 'FCR' and 'FCP'. To identify SlMYB12-linked single nucleotide polymorphisms (SNPs), 'FCR' and 'FCP' were genotyped using a SolCAP Tomato SNP array and CAPS markers (CAPS-456, 531, 13762, and 38123) were developed from the four SNPs (solcap_snp_sl_456, 531, 13762, and 38123) most closely flanking the SlMYB12. These CAPS markers were mapped using $F_2$ plants derived from 'FCR' ${\times}$ 'FCP'. The map positions of the fruit peel color locus (Y) were CAPS-13762 (0 cM) - 456 (11.09 cM) - Y (15.71 cM) - 38123 (17.82 cM) - 531 (30.86 cM), and the DNA sequence of SlMYB12 was physically anchored in the middle of CAPS-456 and CAPS-38123, indicating that fruit peel color in domesticated tomato is controlled by SlMYB12. A total of 64 SolCAP tomato germplasms were evaluated for their fruit peel color and SNPs located between solcap_snp_sl_456 and 38123. Seven SNPs that were detected in this interval were highly conserved for pink-fruited accessions and specific to transparent fruit peel traits, as depicted by a phenetic tree of 64 accessions based on the seven SNPs.

유전자 단위 haplotype을 대변하는 토마토 Tag-SNP 선발 및 웹 데이터베이스 구축 (Tag-SNP selection and online database construction for haplotype-based marker development in tomato)

  • 정혜리;이보미;이봉우;오재은;이정희;김지은;조성환
    • Journal of Plant Biotechnology
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    • 제47권3호
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    • pp.218-226
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    • 2020
  • 유전체 정보가 공공 데이터베이스 내에 빠르게 축적이 되면서 유전체 데이터의 활용도를 높이기 위한 재가공 기술과 공유 기술이 지속적으로 중요해지고 있다. 특히 분자육종을 가속화하기 위해서 다양한 목적에 맞는 분자 마커 개발이 중요하다. 본 연구는 이러한 요구를 해소하기 위해 유전자 단위에서 haplotype을 기본단위로 구분하고 해당 유전자의 haplotype을 대변하는 tag-SNP를 선발하여 분자 마커 등을 개발하는데 사용할 수 있도록 관련 정보를 웹 사이트를 통해서 제공하고자 웹 데이터베이스를 구축하였다. 본 연구를 통해 선발된 각 tag-SNP는 하나의 유전자를 대변할 수 있고, 각 유전자의 haplotype을 구분할 수 있으며, 해당 유전자의 염색체 내 위치 정보, non-synonymous SNP의 정보를 담고 있다. 따라서 기존 무작위 방식으로 선발되어 사용되던 SNP에 비하여 정보력이 높은 tag-SNP를 활용해서 haplotype block을 확장할 수 있을 것이다. Haplotype의 기본 단위를 유전자로 설정함으로써 집단이 바뀜에 따라 발생하는 SNP의 유무, LD block의 크기 등이 변하는 문제점을 극복하고, 표준화된 haplotype library 작성이 가능할 것이며 이는 또한 분자육종을 위한 분자 마커를 선발하는데 활용될 수 있을 것으로 기대된다.

Polymorphisms in the Perilipin Gene May Affect Carcass Traits of Chinese Meat-type Chickens

  • Zhang, Lu;Zhu, Qing;Liu, Yiping;Gilbert, Elizabeth R.;Li, Diyan;Yin, Huadong;Wang, Yan;Yang, Zhiqin;Wang, Zhen;Yuan, Yuncong;Zhao, Xiaoling
    • Asian-Australasian Journal of Animal Sciences
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    • 제28권6호
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    • pp.763-770
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    • 2015
  • Improved meat quality and greater muscle yield are highly sought after in high-quality chicken breeding programs. Past studies indicated that polymorphisms of the Perilipin gene (PLIN1) are highly associated with adiposity in mammals and are potential molecular markers for improving meat quality and carcass traits in chickens. In the present study, we screened single nucleotide polymorphisms (SNPs) in all exons of the PLIN1 gene with a direct sequencing method in six populations with different genetic backgrounds (total 240 individuals). We evaluated the association between the polymorphisms and carcass and meat quality traits. We identified three SNPs, located on the 5' flanking region and exon 1 of PLIN1 on chromosome 10 (rs315831750, rs313726543, and rs80724063, respectively). Eight main haplotypes were constructed based on these SNPs. We calculated the allelic and genotypic frequencies, and genetic diversity parameters of the three SNPs. The polymorphism information content (PIC) ranged from 0.2768 to 0.3750, which reflected an intermediate genetic diversity for all chickens. The CC, CT, and TT genotypes influenced the percentage of breast muscle (PBM), percentage of leg muscle (PLM) and percentage of abdominal fat at rs315831750 (p<0.05). Diplotypes (haplotype pairs) affected the percentage of eviscerated weight (PEW) and PBM (p<0.05). Compared with chickens carrying other diplotypes, H3H7 had the greatest PEW and H2H2 had the greatest PBM, and those with diplotype H7H7 had the smallest PEW and PBM. We conclude that PLIN1 gene polymorphisms may affect broiler carcass and breast muscle yields, and diplotypes H3H7 and H2H2 could be positive molecular markers to enhance PEW and PBM in chickens.

Characterization, detection and identification of transgenic chili pepper harboring coat protein gene that enhances resistance to cucumber mosaic virus

  • Seo, Sang-Gyu;Kim, Ji-Seong;Jeon, Seo-Bum;Shin, Mi-Rae;Kang, Seung-Won;Lee, Gung-Pyo;Hong, Jin-Sung;Harn, Chee-Hark;Ryu, Ki-Hyun;Park, Tae-Sung;Kim, Sun-Hyung
    • Journal of Plant Biotechnology
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    • 제36권4호
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    • pp.384-391
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    • 2009
  • Previously, two events (H15 and B20) of transgenic pepper (Capsicum annuum L.) that enhanced resistance to Cucumber mosaic virus (CMV) by the introduction of CMV coat protein (CP) gene were constructed. Presently, a single copy number of the CP gene was revealed in H15 and B20 by Southern blot. To predict possible unintended effects due to transgene insertion in an endogenous gene, we carried out sequencing of the 5'-flanking region of the CP gene and a Blastbased search. The results revealed that insertion of the transgene into genes encoding putative proteins may occur in the H15 and B20 transgenic event. Mutiplex polymerase chain reaction (PCR) for simultaneous detection and identification of transgenic pepper was conducted with a set of nine primers. Both transgenic event were differentiated from non-transgenic event by the presence of 267 bp and 430 bp PCR products indicative of CP gene specific primer pairs and primer pairs targeting the CP gene and 35S promoter. H15 and B20 uniquely possessed a 390 bp and 596 bp PCR product, respectively. The presence of a 1115 bp product corresponding to intrinsic pepper actin gene confirmed the use of pepper DNA as the PCR template. The primer set and PCR conditions used presently may allow the accurate and simple identification of CMV resistant transgenic pepper.

생쥐 초기배아에서 c-myc Proto-Oncogene Promoter의 기능적 활성화 (Zygotic Expression of c-myc Gene in Mouse Early Embryos: Functional Role of c-myc Promoter)

  • 박기수;강해묵;심찬섭;선웅;김재만;이영기;김경진
    • 한국동물학회지
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    • 제38권4호
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    • pp.550-556
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    • 1995
  • c-myc proto-oncogene은 여러 세포들의 분화와 형질전화에 뿐만 아니라 정상세포의 분열조절에도 관여한다고 알려져왔다. 특히 생쥐의 초기배아에서 c-myc mRNA가 발현되고 antisense c-myc oligomer의 미세주입에 의해 배발생이 억제된다는 연구결과는 c-myc이 초기배아의 발생 및 분열에 관여하는 것을 시사한다. 그러나 최근까지 초기배아에 존재하는 c-myc promoter의 기능적 활성화에 관한 연구는 미진하였다. 이를 위하여, c-myc promoter와 대장균의 lacZ 유전자를 결합시킨 두 종류의 vector(pcmyc-Gall, pcmyc-Ga12)를 만들어 수정란의 전핵에 미세주입한 후, 배 발생에 따른 c-myc promoter의 활성화를 lacZ 유전자의 산물인 $\beta$-galactosidase 에 의한 X-gal 염색으로 조사하였다. 미세주입된 초기 배아는 2세포기 배아를 포함하는 여러 발생단계에서 $\beta$-galactosidase 의 활성을 보였다. 이는 c-myc 유전자가 배아의 게놈유전자로부터 발현되며, 또한 궁극적으로 초기 배아의 발생과정에 중요한 역할을 하고 있음을 시사하고 있다.

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초파리 장조직에서 Caudal 전사조절인자에 의한 matrix metalloproteinase-1 발현 조절 (Regulation of Matrix Metalloproteinase-1 Expression by the Homeodomain Transcription Factor Caudal in Drosophila Intestine)

  • 이신해;황미선;최윤정;김영신;유미애
    • 생명과학회지
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    • 제22권12호
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    • pp.1600-1607
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    • 2012
  • Matrix metalloproteinase (MMP)는 세포외골격의 주요 조절효소로, 배아발생, 혈관생성, 상처치료 및 조직 재생과정에 중요한 인자로 알려져 있다. MMP의 조절 이상은 비정상적 세포외골격 분해로 인해 암 전이와 같은 질병을 일으킨다. 따라서, MMP의 발현과 활성은 엄격하게 조절되고 있다. 최근, 초파리 Mmp1이 소화기관에서 강하게 발현되며, 장줄기세포의 비정상적인 활성을 억제하여 장의 항상성 유지에 중요함을 밝혔다. 하지만, 장조직에서 Mmp1의 발현 조절 기전은 아직 밝혀지지 않았다. 본 연구에서는, 장조직에서 Mmp1의 발현이 장 발생과 항상성 유지에 중요한 Caudal homeobox 유전자에 의해 조절되는지를 연구하였다. GAL4/UAS 조절계를 이용하여 장조직 특이적으로 Caudal의 발현을 감소시켰을 때, Mmp1의 발현이 감소함을 확인하였으며, Caudal을 과발현 시켰을 때, Mmp1의 발현이 증가함을 in vitro와 in vivo 실험 모두에서 확인하였다. 또한, Mmp1 promoter에 Caudal 전사인자 결합 부위가 존재하며, 이 부위가 Mmp1 발현에 중요한 역할을 함을 확인하였다. 이상의 본 연구는, 정상적 혹은 암화 과정에서 Mmp1이 Caudal의 표적 유전자일 수 있음을 의미한다.

섬유소 분해효소 유전자가 도입된 형질전환 돼지 생산 (Production of Transgenic Pig Harboring the Cellulase Digest Gene(CelD))

  • 박진기;이연근;민관식;이창현;이향흔;김광식;장원경;김진회;이훈택
    • 한국가축번식학회지
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    • 제26권2호
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    • pp.87-94
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    • 2002
  • 본 연구는 섬유소분해효소 유전자(CelD)가 도입된 형질전환 돼지를 생산하기 위해 사계절동안 수행하였다. 약 8∼15개월령의 순종의 랜드레이스경산돈 및 미경산돈 126두는 유전자 미세주입을 위한 1세포기 단계의 수정란 채란 및 이식을 위해 사용하였으며, 발정동기화 및 과배란 방법은 PG600 주입 후 9일간 매일 20mg의 altrenogest를 사료에 첨가하여 급여하였다. Altrenogest를 9일간 급여 후 1000IU의 PMSG와 750IU의 hCG를 주입하므로서 과배란을 유도하였다. 미세주입을 위한 유전자는 Rat elasterase promoter에 CelD유전자를 연결하여 준비하였으며, 호르몬 처리후 91두의 공란돈으로부터 1,422개의 난자를 회수하였으며 이중 95.6% (1,359/1,422)는 DNA미세주입을 위해 전핵을 관찰 할 수 있는 1세포기의 수정란이었다. 이중 유전자가 미세주입된 725개의 난자를 35두의 수란돈에 이식하였으며 13두의 임신돈으로부터 65두의 자돈을 생산하였다. 한편 수란돈당 수정란 이식수가 임신율에 미치는 영향을 조사한 결과 약 21∼24개의 수정란을 이식한 구에서 임신율이 50%로 타구의 20.0%(20개 이하)와 33.3%(25개 이상)보다 높았으며, 꼬리조직으로부터 분리된 DNA의 PCR검정결과 65두중 5두가 형질전환 양성 반응을 나타내어 7.69%의 형질전환율을 나타내었다 따라서 본 연구는 생체반응기를 통한 형질전환 돼지생산을 위한 유용한 정보를 제공하게 될 것이다.

Alu-Derived Alternative Splicing Events Specific to Macaca Lineages in CTSF Gene

  • Lee, Ja-Rang;Park, Sang-Je;Kim, Young-Hyun;Choe, Se-Hee;Cho, Hyeon-Mu;Lee, Sang-Rae;Kim, Sun-Uk;Kim, Ji-Su;Sim, Bo-Woong;Song, Bong-Seok;Jeong, Kang-Jin;Lee, Youngjeon;Jin, Yeung Bae;Kang, Philyong;Huh, Jae-Won;Chan, Kyu-Tae
    • Molecules and Cells
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    • 제40권2호
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    • pp.100-108
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    • 2017
  • Cathepsin F, which is encoded by CTSF, is a cysteine proteinase ubiquitously expressed in several tissues. In a previous study, novel transcripts of the CTSF gene were identified in the crab-eating monkey deriving from the integration of an Alu element-AluYRa1. The occurrence of AluYRa1-derived alternative transcripts and the mechanism of exonization events in the CTSF gene of human, rhesus monkey, and crabeating monkey were investigated using PCR and reverse transcription PCR on the genomic DNA and cDNA isolated from several tissues. Results demonstrated that AluYRa1 was only integrated into the genome of Macaca species and this lineage-specific integration led to exonization events by producing a conserved 3' splice site. Six transcript variants (V1-V6) were generated by alternative splicing (AS) events, including intron retention and alternative 5' splice sites in the 5' and 3' flanking regions of CTSF_AluYRa1. Among them, V3-V5 transcripts were ubiquitously expressed in all tissues of rhesus monkey and crab-eating monkey, whereas AluYRa1-exonized V1 was dominantly expressed in the testis of the crab-eating monkey, and V2 was only expressed in the testis of the two monkeys. These five transcript variants also had different amino acid sequences in the C-terminal region of CTSF, as compared to reference sequences. Thus, species-specific Alu-derived exonization by lineage-specific integration of Alu elements and AS events seems to have played an important role during primate evolution by producing transcript variants and gene diversification.

Restriction Enzyme-Mediated Integration 방법으로 확보한 Fusarium oxysporum 형질전환체의 후자리산 생성능 분석 (Fusaric Acid Production in Fusarium oxysporum Transformants Generated by Restriction Enzyme-Mediated Integration Procedure)

  • 이데레사;신진영;손승완;이수형;류재기
    • 식물병연구
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    • 제19권4호
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    • pp.254-258
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    • 2013
  • 후자린산(FA)는 Fusarium 속 균이 생성하는 독소로서 다른 곰팡이독소보다 독성은 낮으나 다른 독소와 중복 오염시 전체 독성을 증진시키는 것으로 알려졌다. 현재까지 FA 생합성 관련 효소나 유전자가 Fusarium oxysporum에서 밝혀지지 않았기 때문에 본 연구에서는 관련 생합성 유전자의 발굴을 위해 제한효소를 통한 무작위 삽입 형질전환방법인 REMI를 이용하여 FA 생성 F. oxysporum 균주의 생합성유전자의 결손을 시도하였다. F. oxysporum 균주 2주를 대상으로 REMI를 시도한 결과, 평균 3.2주 ($1{\mu}g$ DNA 당)의 효율로 7,100주 이상의 형질전환체를 육성하였다. FA 미생성 형질전환체를 스크리닝 하기 위해 FA가 함유된 배양액에서 다양한 식물종자의 발아여부를 조사한 결과, 11종의 종자 중 가장 감수성인 배추종자를 선발하였다. 각 형질전환체는 Czapek-Dox broth에서 3주간 배양한 후 배양여액을 배추종자의 발아여부 검정에 사용하였다. 검정결과 총 5,000여 주의 REMI 형질전환체 중 53주의 배양여액에서 종자가 발아하지 않아, 이들을 FA 미(저) 생성 추정 형질전환체로 선발하였다. 이중 26주의 FA 생성량을 HPLC로 분석한 결과, 2주의 형질전환체에서 모균주 생성량의 1% 이하의 FA가 검출되었다. 이 중 형질전환체 1주로부터 REMI 벡터 삽입 부위 게놈 DNA의 염기서열(252 bp)을 확보하였으며, 이 부위는 F. fujikuroi의 미동정 게놈부위와 93% 유사성이 있음을 확인하였다. 이 부위의 FA생성 관련성 증명을 위해서는 추후 연구가 필요하다.

Induction of Phase I, II and III Drug Metabolism/Transport by Xenobiotics

  • Xu Chang Jiang;Li Christina YongTao;Kong AhNg Tony
    • Archives of Pharmacal Research
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    • 제28권3호
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    • pp.249-268
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    • 2005
  • Drug metabolizing enzymes (DMEs) play central roles in the metabolism, elimination and detoxification of xenobiotics and drugs introduced into the human body. Most of the tissues and organs in our body are well equipped with diverse and various DMEs including phase I, phase II metabolizing enzymes and phase III transporters, which are present in abundance either at the basal unstimulated level, and/or are inducible at elevated level after exposure to xenobiotics. Recently, many important advances have been made in the mechanisms that regulate the expression of these drug metabolism genes. Various nuclear receptors including the aryl hydrocarbon receptor (AhR), orphan nuclear receptors, and nuclear factor-erythoroid 2 p45-related factor 2 (Nrf2) have been shown to be the key mediators of drug-induced changes in phase I, phase II metabolizing enzymes as well as phase III transporters involved in efflux mechanisms. For instance, the expression of CYP1 genes can be induced by AhR, which dimerizes with the AhR nuclear translocator (Arnt) , in response to many polycyclic aromatic hydrocarbon (PAHs). Similarly, the steroid family of orphan nuclear receptors, the constitutive androstane receptor (CAR) and pregnane X receptor (PXR), both heterodimerize with the ret-inoid X receptor (RXR), are shown to transcriptionally activate the promoters of CYP2B and CYP3A gene expression by xenobiotics such as phenobarbital-like compounds (CAR) and dexamethasone and rifampin-type of agents (PXR). The peroxisome proliferator activated receptor (PPAR), which is one of the first characterized members of the nuclear hormone receptor, also dimerizes with RXR and has been shown to be activated by lipid lowering agent fib rate-type of compounds leading to transcriptional activation of the promoters on CYP4A gene. CYP7A was recognized as the first target gene of the liver X receptor (LXR), in which the elimination of cholesterol depends on CYP7A. Farnesoid X receptor (FXR) was identified as a bile acid receptor, and its activation results in the inhibition of hepatic acid biosynthesis and increased transport of bile acids from intestinal lumen to the liver, and CYP7A is one of its target genes. The transcriptional activation by these receptors upon binding to the promoters located at the 5-flanking region of these GYP genes generally leads to the induction of their mRNA gene expression. The physiological and the pharmacological implications of common partner of RXR for CAR, PXR, PPAR, LXR and FXR receptors largely remain unknown and are under intense investigations. For the phase II DMEs, phase II gene inducers such as the phenolic compounds butylated hydroxyanisol (BHA), tert-butylhydroquinone (tBHQ), green tea polyphenol (GTP), (-)-epigallocatechin-3-gallate (EGCG) and the isothiocyanates (PEITC, sul­foraphane) generally appear to be electrophiles. They generally possess electrophilic-medi­ated stress response, resulting in the activation of bZIP transcription factors Nrf2 which dimerizes with Mafs and binds to the antioxidant/electrophile response element (ARE/EpRE) promoter, which is located in many phase II DMEs as well as many cellular defensive enzymes such as heme oxygenase-1 (HO-1), with the subsequent induction of the expression of these genes. Phase III transporters, for example, P-glycoprotein (P-gp), multidrug resistance-associated proteins (MRPs), and organic anion transporting polypeptide 2 (OATP2) are expressed in many tissues such as the liver, intestine, kidney, and brain, and play crucial roles in drug absorption, distribution, and excretion. The orphan nuclear receptors PXR and GAR have been shown to be involved in the regulation of these transporters. Along with phase I and phase II enzyme induction, pretreatment with several kinds of inducers has been shown to alter the expression of phase III transporters, and alter the excretion of xenobiotics, which implies that phase III transporters may also be similarly regulated in a coordinated fashion, and provides an important mean to protect the body from xenobiotics insults. It appears that in general, exposure to phase I, phase II and phase III gene inducers may trigger cellular 'stress' response leading to the increase in their gene expression, which ultimately enhance the elimination and clearance of these xenobiotics and/or other 'cellular stresses' including harmful reactive intermediates such as reactive oxygen species (ROS), so that the body will remove the 'stress' expeditiously. Consequently, this homeostatic response of the body plays a central role in the protection of the body against 'environmental' insults such as those elicited by exposure to xenobiotics.