scholarly journals SNP in DFR1 Coding Sequence Is Tightly Associated with Anthocyanin Accumulation in Cabbage (B. oleracea var. capitata f. alba) at Low Temperature

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 602 ◽  
Author(s):  
Hayoung Song ◽  
Jong-In Park ◽  
Byung-Ho Hwang ◽  
Hankuil Yi ◽  
HyeRan Kim ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Low Temperature ◽  
Anthocyanin Accumulation ◽  
Nucleotide Polymorphism ◽  
High Level Expression ◽  
Single Nucleotide ◽  
Coding Sequence ◽  
Low Level ◽  
High Level

Keeping green leaf color at the time of harvest is one of the important traits for breeding of Brassica oleracea var. capitata f. alba, and this trait is related to low anthocyanin contents. To understand the differential accumulation of anthocyanins in cabbage, we selected high anthocyanin accumulators (HAAs) and low anthocyanin accumulator (LAAs) of cabbages and examined the anthocyanin content and the expression of anthocyanin biosynthesis-related genes. Among many genes investigated, BoDFR1 was found to be closely related to anthocyanin accumulation, even under low temperature (LT) conditions. BoDFR1 sequence analyses between HAAs and LAAs revealed that there is a single nucleotide polymorphism (SNP) (1118T/A) in the coding sequence, which substitutes one amino acid from Leu261 to His261; we named BoDFR1 with His261 substitution as BoDFR1v. This amino acid substitution did not affect dihydroflavonol 4-reductase (DFR) activity and substrate specificity, but the polymorphism showed tight association to the BoDFR1 expression, i.e., high level expression of BoDFR1 and low level expression of BoDFR1v under LT conditions. The high levels of BoDFR1 expression were due to the high levels of BoMYB114 and BobHLH expressions combined with low level expression of BoMYBL2, a repressor MYB. On the other hand, low levels of BoDFR1v expression seemed to be related to very low level expressions of BoMYB114 and BobHLH combined with a high level expression of BoMYBL2. It seems that different expression levels of these regulatory genes for MBW (MYB-bHLH-WD40) complex between HAAs and LAAs regulate BoDFR expression and anthocyanin accumulation. Using a single nucleotide polymorphism (SNP) between BoDFR1 and BoDFR1v, molecular markers for PCR and high resolution melt analyses were developed and validated to distinguish between HAAs and LAAs. Combined use of the BoDFR1 SNP marker with other stress markers, such as a cold tolerant marker, will greatly improve cabbage breeding.

High level of single-nucleotide polymorphism in the rat cyclin B1 gene

1999 ◽  
Vol 10 (6) ◽  
pp. 635-637 ◽  
Author(s):  
Joëlle Petit ◽  
Michèle Rivière ◽  
Josiane Szpirer ◽  
Claude Szpirer
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Cyclin B1 ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
B1 Gene ◽  
High Level

scholarly journals Single Nucleotide Polymorphism in the Cytolethal Distending Toxin B Gene Confers Heterogeneity in the Cytotoxicity of Actinobacillus actinomycetemcomitans

2006 ◽  
Vol 74 (12) ◽  
pp. 7014-7020 ◽  
Author(s):  
Shuichi Nishikubo ◽  
Masaru Ohara ◽  
Masae Ikura ◽  
Katsuo Katayanagi ◽  
Tamaki Fujiwara ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Actinobacillus Actinomycetemcomitans ◽  
Single Amino Acid ◽  
Polymorphism Analysis ◽  
Cytolethal Distending Toxin ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Toxin B

ABSTRACT Clinical Actinobacillus actinomycetemcomitans produces cytolethal distending toxin (CDT) with titers ranging from 102 to 108 U/mg. Single nucleotide polymorphism analysis of the cdt gene in clinical isolates identified a variation of a single amino acid at residue 281 of CdtB, which significantly affected CDT toxicity by modulating the chromatin-degrading activity of CdtB.

scholarly journals Các biến thể gene OsTZF1 liên quan đến khả năng chịu mặn ở giống lúa Đốc Phụng bằng phương pháp giải trình tự bộ gene

2021 ◽  
Vol 57 (4) ◽  
pp. 159-168
Author(s):  
Huỳnh Kỳ ◽  
Đặng Thành Phát Trần ◽  
Thị Kim Phụng Nguyễn ◽  
Văn Quốc Giang ◽  
Văn Mạnh Nguyễn ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Next Generation Sequencing ◽  
Amino Acid ◽  
Next Generation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Generation Sequencing

Trong nghiên cứu này, kỹ thuật giải trình tự thế hệ mới (next generation sequencing) được ứng dụng để giải trình tự của bộ gene 2 giống lúa Đốc Phụng (giống chống chịu mặn) và giống Nếp Mỡ (giống mẫn cảm với mặn), nhằm tìm các chỉ thị phân tử là gene chức năng mà các gene này liên quan đến cơ chế chống chịu mặn có trong giống lúa Đốc Phụng. Kết quả so sánh với bộ gene tham chiếu, bộ gene của giống lúa Đốc Phụng có khoảng 1.918.726 biến thể dạng thay đổi một nucleotide (Single Nucleotide Polymorphism) và và chèn vào khoảng 81.435, mất đi khoảng 81.974. Trong khi đó ở giống Nếp Mỡ, có khoảng 1.931.380 SNP và chèn vào khoảng 88.473, mất đi khoảng 83.190 vùng DNA. Đa số các biến thể xuất hiện ở các vùng không mang chức năng như trước sau và giữa các gene chiếm tỉ lệ trên 75%. Kết quả khảo sát biến thể xuất hiện trong vùng gene OsTZF1 (LOC_Os05g10670.1), có chức năng điều hòa các nhóm gene liên quan đến các yếu tố stress sinh học và phi sinh học, cho thấy ở giống Đốc Phụng có 7 biến thể SNP và có chèn thêm 9 nucleotide mã hóa 3 amino acid arginine khi so với giống Nếp Mỡ dựa trên bộ gene tham chiếu. Thông tin này giúp cho các nhà chọn giống sử dụng nó như chi thị phân tử, chọn tạo giống chống chịu...

scholarly journals Pyrosequencing Using the Single-Nucleotide Polymorphism Protocol for Rapid Determination of TEM- and SHV-Type Extended-Spectrum β-Lactamases in Clinical Isolates and Identification of the Novel β-Lactamase Genes blaSHV-48, blaSHV-105, and blaTEM-155

2008 ◽  
Vol 53 (3) ◽  
pp. 977-986 ◽  
Author(s):  
C. Hal Jones ◽  
Alexey Ruzin ◽  
Margareta Tuckman ◽  
Melissa A. Visalli ◽  
Peter J. Petersen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Sequence Data ◽  
Rapid Determination ◽  
The United States ◽  
Amino Acid Substitutions ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Extended Spectrum ◽  
Rapid Sequence

ABSTRACT TEM- and SHV-type extended-spectrum β-lactamases (ESBLs) are the most common ESBLs found in the United States and are prevalent throughout the world. Amino acid substitutions at a number of positions in TEM-1 lead to the ESBL phenotype, although substitutions at residues 104 (E to K), 164 (R to S or H), 238 (G to S), and 240 (E to K) appear to be particularly important in modifying the spectrum of activity of the enzyme. The SHV-1-derived ESBLs are a less diverse collection of enzymes; however, the majority of amino acid substitutions resulting in an ESBL mirror those seen in the TEM-1-derived enzymes. Pyrosequencing by use of the single-nucleotide polymorphism (SNP) protocol was applied to provide sequence data at positions critical for the ESBL phenotype spanning the bla TEM and bla SHV genes. Three novel β-lactamases are described: the ESBLs TEM-155 (Q39K, R164S, E240K) and SHV-105 (I8F, R43S, G156D, G238S, E240K) and a non-ESBL, SHV-48 (V119I). The ceftazidime, ceftriaxone, and aztreonam MICs for an Escherichia coli isolate expressing bla SHV-105 were >128, 128, and >128 μg/ml, respectively. Likewise, the ceftazidime, ceftriaxone, and aztreonam MICs for an E. coli isolate expressing bla TEM-155 were >128, 64, and > 128 μg/ml, respectively. Pyrosequence analysis determined the true identity of the β-lactamase on plasmid R1010 to be SHV-11 rather than SHV-1, as previously reported. Pyrosequencing is a real-time sequencing-by-synthesis approach that was applied to SNP detection for TEM- and SHV-type ESBL identification and represents a robust tool for rapid sequence determination that may have a place in the clinical setting.

A Single Nucleotide Polymorphism in Pro-Apoptotique Protein BIM Affects Chronic Myeloid Leukaemia Evolution during Imatinib Treatment

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4227-4227
Author(s):  
Vanessa Augis ◽  
Francis Belloc ◽  
Kelly Airiau ◽  
Claudine Chollet ◽  
Francois-Xavier Mahon
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Chronic Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Genotype Frequency ◽  
Imatinib Treatment ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Coding Sequence ◽  
The Impact ◽  
Tyrosin Kinase

Abstract The tyrosin kinase inhibitor imatinib induces apoptosis in chronic myeloid leukaemia (CML) cells. RNA interference experiments have demonstrated that the pro-apoptotic protein BIM (Bcl-2 interacting mediator of cell death) was absolutely essential to this apoptosis. Thus, mutations in BIM sequence could lead to imatinib resistance independently of BCR-ABL mutations. In the current study, we performed BIM coding sequence analysis, using complementary DNA of leukocytes from CML patients mostly secondary resistant to imatinib. A total of 58 patients were analysed: secondary resistant to imatinib (n=40), or on the contrary sensitive to it (n=18). They were in chronic phase (CP, n=43), in accelerated phase (AP, n= 12), or in blastic phase (BP, n=3). Four patients were mutated in the tyrosin kinase domain of BCR-ABL. We did not find any mutation with amino acid change on the coding sequence of BIM. However, we observed a single nucleotide polymorphism (SNP) located in the fifth exon which encode for the BH3 alpha helix part of the protein. The impact of this previously described silent polymorphism C465T (rs724710) has never been studied before. We found the 3 following genotypes : C/C homozygous, T/T homozygous and T/C heterozygous. T/T genotype was the less frequent (It represents about 5% in the European population described in the international Hapmap project). Although not significant (10%, p=0.1468), we observed an increased T/T genotype frequency in the resistant population. In this resistant group, the T/T genotype frequency was increased in advanced phases (AP+BP, 20%) as compared to CP (4%, p=0.0016) or to sensitive cohort (5.6%, p=0.0153) (Fig.1). T/T genotype could affect RNA stability, translation speed and protein folding as described by Kimchi-Sarfaty et al. for the MDR1 gene (Science2007;315:525–8). This genotype can possibly be in linkage disequilibrium with others SNPs or abnormalities (i.e. in the promoter, in splicing sites) in the non coding sequence. The analysis of this polymorphism could be useful to predict the evolution of the disease during imatinib treatment and discriminate resistant patients particularly in advanced phase of the disease. Fig 1 : Genotypes distribution of the C465T polymorphism. Fig 1. Genotypes distribution of the C465T polymorphism. Fig 1. Genotypes distribution of the C465T polymorphism.

scholarly journals The effect of a single nucleotide polymorphism on human α2-antiplasmin activity

Blood ◽  
2007 ◽  
Vol 109 (12) ◽  
pp. 5286-5292 ◽  
Author(s):  
Victoria J. Christiansen ◽  
Kenneth W. Jackson ◽  
Kyung N. Lee ◽  
Patrick A. McKee
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Amino Terminus ◽  
Healthy Population ◽  
Plasma Samples ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genotype Frequencies ◽  
Polymorphic Forms

Abstract The primary inhibitor of plasmin, α2-antiplasmin (α2AP), is secreted by the liver into plasma with Met as the amino-terminus. During circulation, Met-α2AP is cleaved by antiplasmin-cleaving enzyme (APCE), yielding Asn-α2AP, which is crosslinked into fibrin approximately 13 times faster than Met-α2AP. The Met-α2AP gene codes for either Arg or Trp as the sixth amino acid, with both polymorphic forms found in human plasma samples. We determined the Arg6Trp genotype frequency in a healthy population and its effects on Met-α2AP cleavage and fibrinolysis. Genotype frequencies were RR 62.5%, RW 34.0%, and WW 3.5%. The polymorphism related to the percentage of Met-α2AP in plasma was WW (56.4%), RW (40.6%), and RR (23.6%). WW plasma tended to have shorter lysis times than RR and RW plasmas. APCE cleaved purified Met-α2AP(Arg6) approximately 8-fold faster than Met-α2AP(Trp6), which is reflected in Asn-α2AP/Met-α2AP ratios with time in RR, RW, and WW plasmas. Removal of APCE from plasma abrogated cleavage of Met-α2AP. We conclude that the Arg6Trp polymorphism is functionally significant, as it clearly affects conversion of Met-α2AP to Asn-α2AP, and thereby, the rate of α2AP incorporation into fibrin. Therefore, the Arg6Trp polymorphism may play a significant role in governing the long-term deposition/removal of intravascular fibrin.

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