Psoriasis is a chronic inflammatory skin disease that affects 0.1% - 5% depending on the population. PSORS1 is the major susceptibility locus, accounting for approximately 33% - 50% of the genetic component of psorias...Psoriasis is a chronic inflammatory skin disease that affects 0.1% - 5% depending on the population. PSORS1 is the major susceptibility locus, accounting for approximately 33% - 50% of the genetic component of psoriasis among Caucasians. PSORS1 is located within the major histocompatability complex (MHC) locus on 6p21.3. Its position has been refined to hundreds of kilobase and the region located at ～ 100- 200 kb telomeric to human leukocyte antigen (HLA)- C is a very strong candidate. To determine the MHC psoriasis risk haplotype, we screened the whole 46 kb interval for single- nucleotide polymorphisms (SNP) and identified 138 SNP. We genotyped 29 SNP throughout this region in psoriatic nuclear families. We calculated the frequency of haplotypesgenerated bythe 29 SNP using all genotyped founder individuals and found four common haplotype with frequency >0.10. We then used SNP- tagger to derive the best six SNP and fed these into Transmit using 148 nuclear families. We found that CTGGAC haplotype is a single- point score haplotypes telomeric to HLA- C and gives a 1 df, χ 2 of 50.27 (P < 0.0001). Most importantly the six selected SNP accurately tagged the most common haplotype found in this region. Moreover, using the same program (Transmit) we show that the association with CTGGAC is higher than the one with HLA- Cw6 (χ 2=10.53; P=0.0051). Our results give scores as high as the highest single- point scores suggesting that it is unlikely to be able to discriminate the origin of the association on this analysis on strength of association.展开更多
Chrysoperla externa is found in environment, their populations may experience several Brazilian agroecosystems and feeds on many agricultural pests. In each different environmental pressures that can favor the emergen...Chrysoperla externa is found in environment, their populations may experience several Brazilian agroecosystems and feeds on many agricultural pests. In each different environmental pressures that can favor the emergence of genetic mutations and interfere in insect＇s ecological plasticity. Such genetic phenomena can be observed through the use of molecular markers, in particular mitochondrial genes, which are easy to handle and extract. The aim of this work was to study haplotype diversity of Chrysoperla externa in the cities of Jaboticabal （SP）, Brotas （SP）, Rifaina （SP）, Sao Carlos （SP）, Sao Jose dos Campos （SP） and Sao Sebastiao do Paraiso （MG）, and evaluate the degree of genetic differentiation between these populations. Two mitochondrial genes were sequenced to compare these populations. It was found that there were eight haplotypes, six mutations for cytochrome c oxidase subunit 1 （COl） gene and a greater haplotype diversity was found in Brotas and Sao Sebastiao do Paraiso. There were four mutations and six haplotypes for 16S gene and the highest haplotype diversity was found in the city of San Sebastiao do Paraiso. No pattern of haplotype distribution for the populations analyzed was found. The genetic distance between populations of C. externa was not significant, showing that they are genetically compatible.展开更多
The C++ program: Hapseeker was developed to analyze DNA or RNA sequence, besides, Hapseeker could be used to identify haplotype, calculate frequency of each haplotype as well as find variable site quickly. Moreover, H...The C++ program: Hapseeker was developed to analyze DNA or RNA sequence, besides, Hapseeker could be used to identify haplotype, calculate frequency of each haplotype as well as find variable site quickly. Moreover, Hapseeker had many advantages such as simple operation, rapid running speed and high accuracy.展开更多
文摘Psoriasis is a chronic inflammatory skin disease that affects 0.1% - 5% depending on the population. PSORS1 is the major susceptibility locus, accounting for approximately 33% - 50% of the genetic component of psoriasis among Caucasians. PSORS1 is located within the major histocompatability complex (MHC) locus on 6p21.3. Its position has been refined to hundreds of kilobase and the region located at ～ 100- 200 kb telomeric to human leukocyte antigen (HLA)- C is a very strong candidate. To determine the MHC psoriasis risk haplotype, we screened the whole 46 kb interval for single- nucleotide polymorphisms (SNP) and identified 138 SNP. We genotyped 29 SNP throughout this region in psoriatic nuclear families. We calculated the frequency of haplotypesgenerated bythe 29 SNP using all genotyped founder individuals and found four common haplotype with frequency >0.10. We then used SNP- tagger to derive the best six SNP and fed these into Transmit using 148 nuclear families. We found that CTGGAC haplotype is a single- point score haplotypes telomeric to HLA- C and gives a 1 df, χ 2 of 50.27 (P < 0.0001). Most importantly the six selected SNP accurately tagged the most common haplotype found in this region. Moreover, using the same program (Transmit) we show that the association with CTGGAC is higher than the one with HLA- Cw6 (χ 2=10.53; P=0.0051). Our results give scores as high as the highest single- point scores suggesting that it is unlikely to be able to discriminate the origin of the association on this analysis on strength of association.
文摘Chrysoperla externa is found in environment, their populations may experience several Brazilian agroecosystems and feeds on many agricultural pests. In each different environmental pressures that can favor the emergence of genetic mutations and interfere in insect＇s ecological plasticity. Such genetic phenomena can be observed through the use of molecular markers, in particular mitochondrial genes, which are easy to handle and extract. The aim of this work was to study haplotype diversity of Chrysoperla externa in the cities of Jaboticabal （SP）, Brotas （SP）, Rifaina （SP）, Sao Carlos （SP）, Sao Jose dos Campos （SP） and Sao Sebastiao do Paraiso （MG）, and evaluate the degree of genetic differentiation between these populations. Two mitochondrial genes were sequenced to compare these populations. It was found that there were eight haplotypes, six mutations for cytochrome c oxidase subunit 1 （COl） gene and a greater haplotype diversity was found in Brotas and Sao Sebastiao do Paraiso. There were four mutations and six haplotypes for 16S gene and the highest haplotype diversity was found in the city of San Sebastiao do Paraiso. No pattern of haplotype distribution for the populations analyzed was found. The genetic distance between populations of C. externa was not significant, showing that they are genetically compatible.
文摘对浙江瑞安、福建宁德、福建东张水库3个地理群体共31例香鱼(Plecoglossus altivelis)的线粒体细胞色素b(Cyt b)基因和线粒体D-loop区序列进行了PCR扩增、序列测定、核苷酸组成和多态性分析。Cytb基因中,A、T、C和G4种核苷酸的比例分别为19.72%、29.71%、32.25%和18.32%,A+T含量为49.43%,G+C含量为50.57%。D-loop区序列中,A、T、C和G4种核苷酸的比例分别为29.99%、29.29%、23.80%和16.92%,A+T含量为59.28%,G+C含量为40.72%。在长度为1141bp的Cytb基因序列中,仅存在1个变异位点,核苷酸多样性指数(π值)为0.00028,31个样本中仅出现两种单倍型;857 bp 长的D-loop区序列中,仅存在5个变异位点,核苷酸多样性指数(π值)为0.00199,仅出现5种单倍型。这表明闽浙地区香鱼的遗传多样性水平很低,应当加大对香鱼的保护力度。
基金Supported by the Pilot Project of the Knowledge Innovation Program(0654221211)~~
文摘The C++ program: Hapseeker was developed to analyze DNA or RNA sequence, besides, Hapseeker could be used to identify haplotype, calculate frequency of each haplotype as well as find variable site quickly. Moreover, Hapseeker had many advantages such as simple operation, rapid running speed and high accuracy.
