scholarly journals Tunable Blinking Kinetics of Cy5 for Precise DNA Quantification and Single-Nucleotide Difference Detection

2008 ◽  
Vol 95 (2) ◽  
pp. 729-737 ◽  
Author(s):  
Hsin-Chih Yeh ◽  
Christopher M. Puleo ◽  
Yi-Ping Ho ◽  
Vasudev J. Bailey ◽  
Teck Chuan Lim ◽  
...  
Keyword(s):  
Dna Quantification ◽  
Nucleotide Difference ◽  
Single Nucleotide ◽  
Difference Detection ◽  
Kinetics Of

One single nucleotide difference alters the differential expression of spliced RNAs between HBV genotypes A and D

2013 ◽  
Vol 174 (1-2) ◽  
pp. 18-26 ◽  
Author(s):  
Chien-Chiao Huang ◽  
Tzer-Min Kuo ◽  
Chau-Ting Yeh ◽  
Cheng-po Hu ◽  
Ya-Ling Chen ◽  
...  
Keyword(s):  
Differential Expression ◽  
Nucleotide Difference ◽  
Single Nucleotide ◽  
Hbv Genotypes

scholarly journals Bottom-up single-molecule strategy for understanding subunit function of tetrameric β-galactosidase

2018 ◽  
Vol 115 (33) ◽  
pp. 8346-8351 ◽  
Author(s):  
Xiang Li ◽  
Yu Jiang ◽  
Shaorong Chong ◽  
David R. Walt
Keyword(s):  
Single Molecule ◽  
Wild Type ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Single Molecule Level ◽  
Subunit Function ◽  
Enzyme Molecules ◽  
Individual Enzyme ◽  
Kinetics Of

In this paper, we report an example of the engineered expression of tetrameric β-galactosidase (β-gal) containing varying numbers of active monomers. Specifically, by combining wild-type and single-nucleotide polymorphism plasmids at varying ratios, tetrameric β-gal was expressed in vitro with one to four active monomers. The kinetics of individual enzyme molecules revealed four distinct populations, corresponding to the number of active monomers in the enzyme. Using single-molecule-level enzyme kinetics, we were able to measure an accurate in vitro mistranslation frequency (5.8 × 10−4 per base). In addition, we studied the kinetics of the mistranslated β-gal at the single-molecule level.

scholarly journals Isolation of Salmonella enterica subspecies enterica serovar Paratyphi B dT+, or Salmonella Java, from Indonesia and alteration of the d-tartrate fermentation phenotype by disrupting the ORF STM 3356

2006 ◽  
Vol 55 (12) ◽  
pp. 1661-1665 ◽  
Author(s):  
Kyung Ho Han ◽  
Seon Young Choi ◽  
Je Hee Lee ◽  
Hyejon Lee ◽  
Eun Hee Shin ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Reference Strain ◽  
Multidrug Resistant ◽  
Nucleotide Difference ◽  
Single Nucleotide ◽  
Functional Product ◽  
Paratyphi B ◽  
In Trans ◽  
Paratyphoid Fever ◽  
Discrimination Method

Salmonella enterica subspecies enterica serovar Paratyphi B [O1,4,(5),12 : Hb : 1,2] can cause either an enteric fever (paratyphoid fever) or self-limiting gastroenteritis in humans. The d-tartrate non-fermenting variant S. enterica subsp. enterica serovar Paratyphi B dT− (S. Paratyphi B) is the causative agent of paratyphoid fever, and the d-tartrate fermenting variant S. enterica subsp. enterica serovar Paratyphi B dT+ (S. Paratyphi B dT+; formerly called Salmonella Java) causes gastroenteritis. S. Java is currently recognized as an emerging problem worldwide. Twelve dT+ S. Java isolates were collected in Indonesia between 2000 and 2002. One-third of them contained Salmonella genomic island 1 (SGI1), which gives the multidrug-resistant phenotype to the bacteria. In this study, a PCR-based method to detect a single nucleotide difference responsible for the inability to ferment d-tartrate, reported elsewhere, was validated. The d-tartrate fermenting phenotype of S. Java was converted to the non-fermenting phenotype by the disruption of the ORF STM 3356, and the d-tartrate non-fermenting phenotype of the ORF STM 3356-disrupted strain and the dT− reference strain was changed to the dT+ phenotype by complementing ORF STM 3356 in trans. The results show that the dT+ phenotype requires a functional product encoded by STM 3356, and support the use of the PCR-based discrimination method for S. Paratyphi B and S. Java as the standard differentiation method.

Reaktionen und relative Affinitäten zwischen verschiedenen Nucleotiden und F-Actin unter Ultraschall

1965 ◽  
Vol 20 (10) ◽  
pp. 977-989 ◽  
Author(s):  
Irene Kakol ◽  
Hans H. Weber
Keyword(s):  
Actin Filaments ◽  
Mechanical Treatment ◽  
Quaternary Structure ◽  
Optimal Conditions ◽  
Single Nucleotide ◽  
Teflon Piston ◽  
Affinity Constants ◽  
Relative Affinity ◽  
Kinetics Of ◽  
Zero Time

1. Like the polymerization of G-actin, the repolymerization of F-actin treated with USV occurs in the presence of every nucleosidetriphosphate (NTP) as well as nucleosiddiphosphate (NDP) that have been investigated.2. At 4°C solutions of F-actin exchange about 9 per cent of their bound nucleotide instantaneously and about 7 percent during the next 24 hours even then when they are not mechanically treated.3. On the other hand, every nucleotide is exchanged with considerable velocity if the F-actin solution at pH ~ 7 and 4°C is mechanically treated with USV or in the homogenisator. The rate of exchange decreases considerably if the KCl of the solution is replaced by MgCl2. Moreover, the rate of exchange decreases with the increase of the concentration of F-actin from 1,5·10-5 M to 5·10-5 M if the solution is treated with USV (but not when treated in the homogenisator).4. The exchanged amounts of all investigated nucleotides are identical if during the mechanical treatment the nucleotides are present in a concentration of ≧ 10-3 M. Under optimal conditions (KCl, 1,6 ·10-5 M F-actin) either in a USV-period of 40′ or after a thousand movements of the teflon piston in the homogenisator, the exchange of the nucleotides reaches an average of 90 per cent. Even after mechanical treatment one, F-actin still binds one mole nucleotide.5. The kinetics of exchange is monomolecular in any case.6. If the nucleotide entering by exchange is a triphosphate one phosphate is split off. The kinetics of the splitting is linear.7. At zero time the rate of exchange and that of splitting are virtually the same, but later the measured rate of exchange lags more and more behind the rate of splitting. At a given moment the ratio of split nucleotide, to exchanged nucleotide is the ratio one would expect under the following two conditions: (a) The single nucleotide ion is split only during the regeneration of a break of the F-actin filament if it has been bound to the point of breaking immediately before the regeneration, (b) The breaks between the single monomeres are statistically distributed over the lengths of the filament (i. e. the interaction of all monomers is of equal strength).8. If the exchange occurs in the presence of two competing nucleotides the ratio of the affinities of the competing nucleotides to F-actin can be calculated. Thus it has been found that the relative affinities decrease in the following sequence: ATP>ITP>ADP>IDP>GTP>CTP. This sequence coincides with that of the relative affinity constants to G-actin; in addition the numerical values of the affinity constants to F-actin and to G-actin are similar.9. The same rules obey the binding of the different nucleotides to G-actin and to F-actin as well as the splitting of the nucleotides during the polymerization of G-actin and during the repolymerization of broken F-actin filaments. Thus the seemingly different behaviour of G-actin nucleotide compounds and of F-actin nucleotide compounds becomes the same or nearly so if the steric hindrance of the nucleotide reactions (because of the special quaternary structure of F-actin) is removed by mechanical treatment such as USV or treatment in the homogenisator.

Ultrasensitive SERS detection of highly homologous miRNAs by generating 3D organic-nanoclusters and a functionalized chip with locked nucleic acid probes

2018 ◽  
Vol 54 (95) ◽  
pp. 13431-13434 ◽  
Author(s):  
Mengting Zhu ◽  
Zhaomei Sun ◽  
Zhen Zhang ◽  
Shusheng Zhang
Keyword(s):  
Nucleic Acid ◽  
Locked Nucleic Acid ◽  
Nucleotide Difference ◽  
Single Nucleotide ◽  
Nucleic Acid Probes ◽  
Sers Detection ◽  
New Finding

Herein, a new finding is reported that 3D organic-nanoclusters (3DONs) with superior SERS properties as an original reporter could accurately and sensitively distinguish microRNAs (miRNAs) with highly similar sequences, even with a single-nucleotide difference.

scholarly journals Sequence, infectivity and replication kinetics of SARS-CoV-2 isolated from COVID-19 patients in Canada

2020 ◽  
Author(s):  
Arinjay Banerjee ◽  
Jalees A. Nasir ◽  
Patrick Budylowski ◽  
Lily Yip ◽  
Patryk Aftanas ◽  
...  
Keyword(s):  
Mononuclear Cells ◽  
Productive Infection ◽  
Nucleotide Polymorphisms ◽  
Peripheral Blood Mononuclear ◽  
Single Nucleotide ◽  
Infection Models ◽  
Wide Range ◽  
Kinetics Of

ABSTRACTSARS-CoV-2 emerged in December 2019 in Wuhan, China and has since infected over 1.5 million people, of which over 107,000 have died. As SARS-CoV-2 spreads across the planet, speculations remain about the range of human cells that can be infected by SARS-CoV-2. In this study, we report the isolation of SARS-CoV-2 from two COVID-19 patients in Toronto, Canada. We determined the genomic sequences of the two isolates and identified single nucleotide changes in representative populations of our virus stocks. More importantly, we tested a wide range of human immune cells for productive infection with SARS-CoV-2. Here we confirm that human primary peripheral blood mononuclear cells (PBMCs) are not permissive to SARS-CoV-2. As SARS-CoV-2 continues to spread globally, it is essential to monitor small nucleotide polymorphisms in the virus and to continue to isolate circulating viruses to determine cell susceptibility and pathogenicity using in vitro and in vivo infection models.

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