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71.
Akihiro Kuno Yoshihisa Ikeda Shinya Ayabe Kanako Kato Kotaro Sakamoto Sayaka R. Suzuki Kento Morimoto Arata Wakimoto Natsuki Mikami Miyuki Ishida Natsumi Iki Yuko Hamada Megumi Takemura Yoko Daitoku Yoko Tanimoto Tra Thi Huong Dinh Kazuya Murata Michito Hamada Masafumi Muratani Atsushi Yoshiki Fumihiro Sugiyama Satoru Takahashi Seiya Mizuno 《PLoS biology》2022,20(1)
Genome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes.Genome editing can introduce designed mutations into a target genomic site, but also into unintended off-target sites. DAJIN, a novel nanopore sequencing data analysis tool, identifies and quantifies allele numbers and their mutation patterns, reporting consensus sequences and visualizing mutations in alleles at single-nucleotide resolution. 相似文献
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74.
Akihiro Kinoshita Tomoo Tamura Chiharu Aoki Tohru Nakanishi Shizuo Sobue Fujio Suzuki Kojiro Takahashi Masaharu Takigawa 《Cell biology international》1995,19(8):647-654
Endothelin (ET) receptors on chondrocytes were demonstrated using cultured rabbit costal chondrocytes. After crosslinking the receptors on the cells with 125 I-ET-1, two major bands of 43 kDa and 46 kDa were separated by SDS-PAGE. Scatchard analysis demonstrated two classes of ET receptors with Kd values of 1 × 10?10 M and 5 × 10?9 M. The numbers of high- and low- affinity receptors were 1 × 104 and 2 × 105 per cell, respectively. The binding of ET-1 to chondrocytes was increased by treatment with PTH, DBcAMP, TGF-β1, IL-1β, RA and EGF. ET-1 stimulated DNA synthesis in cultured rabbit chondrocytes. ET-1 also stimulated calcium incorporation through the cell membrane of chondrocytes. These findings indicate that ET-1 has a physiological effect on chondrocytes via its receptors on the cells. 相似文献
75.
Kaori Tsukakoshi Yasuko Yamagishi Mana Kanazashi Kenta Nakama Daiki Oshikawa Nasa Savory Akimasa Matsugami Fumiaki Hayashi Jinhee Lee Taiki Saito Koji Sode Kanjana Khunathai Hitoshi Kuno Kazunori Ikebukuro 《Nucleic acids research》2021,49(11):6069
Aptamers can control the biological functions of enzymes, thereby facilitating the development of novel biosensors. While aptamers that inhibit catalytic reactions of enzymes were found and used as signal transducers to sense target molecules in biosensors, no aptamers that amplify enzymatic activity have been identified. In this study, we report G-quadruplex (G4)-forming DNA aptamers that upregulate the peroxidase activity in myoglobin specifically for luminol. Using in vitro selection, one G4-forming aptamer that enhanced chemiluminescence from luminol by myoglobin''s peroxidase activity was discovered. Through our strategy—in silico maturation, which is a genetic algorithm-aided sequence manipulation method, the enhancing activity of the aptamer was improved by introducing mutations to the aptamer sequences. The best aptamer conserved the parallel G4 property with over 300-times higher luminol chemiluminescence from peroxidase activity more than myoglobin alone at an optimal pH of 5.0. Furthermore, using hemin and hemin-binding aptamers, we demonstrated that the binding property of the G4 aptamers to heme in myoglobin might be necessary to exert the enhancing effect. Structure determination for one of the aptamers revealed a parallel-type G4 structure with propeller-like loops, which might be useful for a rational design of aptasensors utilizing the G4 aptamer-myoglobin pair. 相似文献
76.
Common marmosets vocalize phee calls as isolation calls, which seem to facilitate their reunion with family groups. To identify multiple acoustic properties with different time courses, we examined acoustic modulations of phees during different social contexts of isolation. Subject marmosets were totally isolated in one condition, were visually isolated and could exchange vocalizations in another condition, and were visually isolated and subsequently totally isolated in a third condition. We recorded 6,035 phees of 10 male–female marmoset pairs and conducted acoustic analysis. The marmosets frequently vocalized phees that were temporally elongated and louder during isolation, with varying time courses of these changes in acoustic parameters. The vocal rates and sound levels of the phees increased as soon as the marmosets saw their pair mates being taken away, and then gradually calmed down. The phee duration was longer in conditions during which there were no vocal responses from their pair mates. Louder vocalizations are conspicuous and seem to be effective for long‐distance transmission, whereas shorter call duration during vocal exchanges might avoid possible vocal overlap between mates. Am. J. Primatol. 72:681–688, 2010. © 2010 Wiley‐Liss, Inc. 相似文献
77.
Akihiro Kondo John Sidney Scott Southwood Marie-France del Guercio Ettore Appella Hiroshi Sakamoto Howard M. Grey Esteban Celis Robert W. Chesnut Ralph T. Kubo A. Sette 《Immunogenetics》1997,45(4):249-258
Previous studies have defined two different peptide binding motifs specific for HLA-A
*
0101. These motifs are characterized by the presence of tyrosine (Y) at the C-termini of 9-mer and 10-mer peptides, and either
a small polar or hydrophobic (S, T, M) residue in position 2, or a negatively charged (D or E) residue in position 3. In this
study, the structural requirements for peptide binding to A
*
0101 have been further analyzed by examining the binding capacity of large sets of peptides corresponding to naturally occurring
sequences which bore one or the other of these two A
*
0101-specific motifs. By correlating the presence of specific residue types at each position along the peptide sequence with increased
(or decreased) binding affinity, the prominent influence of secondary anchor residues was revealed. In most cases, the two
anchors in positions 2 and 3 appear to act synergistically. With the exception of the DE3 submotif in 9-mer peptides, a positive role for aromatic residues in position 1 and the center of the peptide (positions
4 or 5 of 9- or 10-mer peptides, respectively), and proline at C-3, were also consistently detected. However, secondary anchor
residues also appear to differ significantly between the two different submotifs, demonstrating that A
*
0101 can utilize alternative modes in binding its peptide ligands. According to these analyses, specific refined submotifs were
also established, and their merit verified by independent sets of potential A
*
0101 binding peptides. Besides providing useful insight into the nature of the interaction of the A
*
0101 allele with its peptide ligands, such refined motifs should also facilitate accurate prediction of potential A
*
0101-restricted peptide epitopes.
Received: 16 July 1996 / Revised: 18 September 1996 相似文献
78.
Kumagai H Koizumi A Suda A Sato N Sakurai H Kumagai H 《Bioscience, biotechnology, and biochemistry》2004,68(7):1598-1600
Soybean globulins were deamidated after removing phytate using ion-exchange resins, and then hydrolyzed by digestive enzymes. The phytate-removed deamidated soybean globulins (PrDS) retained high calcium-binding ability even after the hydrolysis by digestive enzymes. PrDS and its hydrolysates enhanced calcium absorption from the small intestine when injected into the small intestine together with a calcium solution. 相似文献
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