scholarly journals Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

Science ◽  
2018 ◽  
Vol 362 (6416) ◽  
pp. 839-842 ◽  
Author(s):  
Lucas B. Harrington ◽  
David Burstein ◽  
Janice S. Chen ◽  
David Paez-Espino ◽  
Enbo Ma ◽  
...  
Keyword(s):  
Amino Acids ◽  
Adaptive Immunity ◽  
Metagenomic Data ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Large Size ◽  
Rna Targeting ◽  
Sequence Requirements ◽  
Single Effector ◽  
Cas Proteins

CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 to 1400 amino acids) has been considered essential to their specific DNA- or RNA-targeting activities. Here we present a set of CRISPR-Cas systems from uncultivated archaea that contain Cas14, a family of exceptionally compact RNA-guided nucleases (400 to 700 amino acids). Despite their small size, Cas14 proteins are capable of targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements. Moreover, target recognition by Cas14 triggers nonspecific cutting of ssDNA molecules, an activity that enables high-fidelity single-nucleotide polymorphism genotyping (Cas14-DETECTR). Metagenomic data show that multiple CRISPR-Cas14 systems evolved independently and suggest a potential evolutionary origin of single-effector CRISPR-based adaptive immunity.

scholarly journals Leptin gene polymorphism of Ongole Grade cattle based on single nucleotide polymorphism

2018 ◽  
Vol 43 (4) ◽  
pp. 309
Author(s):  
N. Hilmia ◽  
D. Rahmat ◽  
D. Dudi
Keyword(s):  
Amino Acids ◽  
Single Nucleotide Polymorphism ◽  
Gene Polymorphism ◽  
Direct Sequencing ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Specific Allele ◽  
Polymerase Chain

Point mutation on exon 2 of leptin gene, which changes amino acid encoding from Arginine to Cysteine, may alters the physiological function of the leptin hormone. This study aimed to identify leptin gene polymorphism of Ongole Grade (OG) cattle based on Single Nucleotide Polymorphism (SNP). The DNA sample was taken from 48 head of OG cattle at Balai Pengembangan Perbibitan Ternak Sapi Potong(BPPT SP) Cijeungjing West Java, which was isolated from white blood cell using the high salt method. Amplification of DNA was done by Polymerase Chain Reaction (PCR), followed by direct sequencing to obtain nucleotide sequence. The SNP analysis was carried out from alignment of sequencing result using Bioedit and MEGA 5.2 program. The results indicated in exon 2 leptin gene of OG cattle there was one synonymous SNPs that did not changeamino acids Serine encoding on g.1025T >C/S17S, while two non synonymous SNPaltered amino acids encoding, those were g.1047C> T /R25C and g.1048G>A/R25H. Those mutations changed amino acids encoding from Arginine to Cysteine and Arginine to Histidine respectively.In OG cattle, the frequency of A allele (44.8%) was higher than C allele (33.3%) and T allele (21.9%). Six genotypes were also identified, i.e. AA (41.7%), CC (20.8%), CT (20.8%), CA(4.2%), TT (10.4%) and TA (2.1 %). Heterozigosity of OG cattle based on leptin gene was 0.65 that was a high category. The A allele was a specific allele on Indonesian local cattle.

scholarly journals Polymorphism at four-fold degenerate site, but not at the intergenic regions, explains nucleotide compositional strand asymmetry in bacteria

2021 ◽  
Author(s):  
Piyali Sen ◽  
Ruksana Aziz ◽  
Soumita Das ◽  
Nima Dondu Namsa ◽  
Ramesh Chandra Deka ◽  
...  
Keyword(s):  
Amino Acids ◽  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Codon Usage Bias ◽  
Nucleotide Composition ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Strand Asymmetry ◽  
Intergenic Regions ◽  
Polymorphism Pattern

We investigated single nucleotide polymorphism in intergenic regions (IRs) and four-fold degenerate sites (FFS) in genomes of three γ-Proteobacteria and two Firmicutes to understand the mechanism of nucleotide compositional asymmetry between the leading and the lagging strands. Pattern of the polymorphism spectra were alike regarding transitions but variable regarding transversions in the IRs of these bacteria. Contrasting trends of complementary polymorphisms such as C->T vs G->A as well as A->G vs T->C in the IRs vindicated similar replication-associated strand asymmetry regarding cytosine and adenine deamination, respectively, across these bacteria. Surprisingly, the polymorphism pattern at FFS was different from that of the IRs and its frequency was always more than the IRs in these bacteria. Further, the polymorphism patterns within a bacterium were inconsistent across the five amino acids, which neither the replication nor the transcription-associated mutations could explain. However, the polymorphism at FFS coincided with amino acid specific codon usage bias in the five bacteria. Further, strand asymmetry in nucleotide composition could be explained by the polymorphism at FFS, not at the IRs. Therefore, polymorphisms at FFS might not be treated as nearly neutral unlike that in IRs in these bacteria.

A single nucleotide polymorphism in the bovine β-casein promoter region across different bovine breeds

2006 ◽  
Vol 73 (2) ◽  
pp. 193-196 ◽  
Author(s):  
Aileen F Keating ◽  
Terry J Smith ◽  
R Paul Ross ◽  
Michael T Cairns
Keyword(s):  
Amino Acids ◽  
Single Nucleotide Polymorphism ◽  
Protein Content ◽  
Milk Production ◽  
Genetic Variants ◽  
Promoter Region ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Coding Sequence

The bovine β-casein (CSN2) gene has been shown to span a region of 8·5 kb, containing nine exons and eight intervening introns (Bonsing et al. 1988; Martin et al. 2002). The exons range in size from 24 to 498 bp; the introns, however, are much larger and account for 85% of the gene. Twelve genetic variants in the coding sequence of the β-casein gene have been reported (Farrell et al. 2004). The A2 allele of the β-casein gene has been associated with a higher milk production (Lin et al. 1986; Bech & Kristiansen, 1990) while the B variant has been associated with an increase in protein content and better cheesemaking properties (Marziali & Ng-Hang-Kwai, 1986). The β-casein gene codes for a protein of 209 amino acids with varying regions at codons 67, 106 and 122. The A1 variant differs from A2 at position 67, where a histidine replaces a proline (Lien et al. 1992). The β-casein A2 variant has histidine and the A3 variant has glycine at position 106 (Lien et al. 1992); the β-casein A2 variant has serine at position 122 and the β-casein B variant has arginine at this codon (Stewart et al. 1987; Damiani et al. 1992).

scholarly journals Developmentof 84 single nucleotide polymorphism (SNP) markers for the three-spot swimming crab (Portunus sanguinolentus) by using RAD appoach Guidong Miao1,2,3 Feng Wang1,2,3 Jihua Guo1,2,3, Pei Zhang1,2,3 Hongyu Ma4

2021 ◽  
Author(s):  
Guidong Miao ◽  
Feng Wang ◽  
Jihua Guo ◽  
Pei Zhang ◽  
Hongyu Ma
Keyword(s):  
Dna Sequences ◽  
Average Frequency ◽  
Snp Markers ◽  
Swimming Crab ◽  
Nucleotide Polymorphism ◽  
Base Pairs ◽  
Single Nucleotide ◽  
Large Size ◽  
Pcr Products ◽  
Hardy Weinberg Equilibrium

Abstract The three-spot swimming crab (Portunus sanguinolentus) is one of most important large size economic crab in China. In this study, we first isolated and characterized a set of 84 SNP loci in P. sanguinolentus. 10 pairs of primers PCR products were sequenced and a total of 3181bp high-quality DNA sequences were obtained from which 84 polymorphic SNP loci were identifed and 84 SNP loci were identified and accurated genotyped. The average frequency of SNP loci was one locus every 38 base pairs in P. sanguinolentus genome. Of these 84 SNP loci, each had bi-alleles with the minor allele frequency ranging from 0.0167 to 0.5000. The observed heterozygosity varied from 0.0333 to 0.7143, while the expected heterozygosity ranged from 0.0333 to 0.5085 per locus. 51 loci showed low variation (HO ≤ 0.3) and fourteen SNP loci showed high variation (HO ≥ 0.5). Among 84 SNP loci, 11 loci showed significant deviation from Hardy–Weinberg Equilibrium. The SNP markers developed herein will provide valuable information for elucidating population genetic diversity, population dynamics, and conservation genetics of this germplasm resource and other related crab species.

UTILIZATION OF DNA MARKERS FOR EVALUATING AMYLOSE CONTENT OF GRAIN IN RICE

2013 ◽  
Vol 83 (5) ◽  
Author(s):  
Dương Thanh Thủy ◽  
Taiichiro Ookawa
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amylose Content ◽  
Waxy Gene ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Branching Enzymes ◽  
Wx Gene ◽  
High Amylose ◽  
Suitable Marker ◽  
Granule Bound Starch Synthase

The sensory and functional properties of rice are predominantly associated with its amylose content. Granule-bound starch synthase (GBSS) encoded by the Waxy (Wx) gene determines the synthesis of amylose, while starch branching enzymes encoded by Sbe genes are involved in the formation of amylopectin. Some studies have demonstrated that Wx gene is the major controller of amylose content but there are one or more modifying genes affecting the amylose content. Three markers,  microsatellite, Single – nucleotide – polymorphism (G/T SNP) in Wx gene and Single – nucleotide – polymorphism (T/C SNP) in Sbe1 gene, were tested for their association with amylose content using sixty-nine  rice accessions from twenty countries. Of the three markers, two markers in Wx gene are significantly associated with amylose content. The combination of two markers in Wx gene (haplotypes) explained 83.8% of the variation in amylose content and discriminated the three market classes of glutinous, low, intermediate and high amylose content of rice from each other. And T/C SNP in Sbe1 locus was not a suitable marker for amylose content. Keywords: marker, amylose content, Waxy gene.

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