dna fragments
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Diversity ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 53
Author(s):  
Luca Vecchioni ◽  
Andrew C. Ching ◽  
Federico Marrone ◽  
Marco Arculeo ◽  
Peter J. Hundt ◽  
...  

We used a multi-locus phylogenetic approach (i.e., combining both mitochondrial and nuclear DNA fragments) to address some long-standing taxonomic inconsistencies within the diverse fish clade of Combtooth Blennies (Blenniidae—unranked clade Almadablennius). The obtained phylogenetic trees revealed some major inconsistencies in the current taxonomy of Parablennini, such as the paraphyletic status of the Salaria and Parablennius genera, casting some doubt regarding their actual phylogenetic relationship. Furthermore, a scarce-to-absent genetic differentiation was observed among the three species belonging to the genus Chasmodes. This study provides an updated taxonomy and phylogeny of the former genus Salaria, ascribing some species to the new genus Salariopsis gen. nov., and emphasizes the need for a revision of the genus Parablennius.


2022 ◽  
Vol 16 (1) ◽  
pp. 1
Author(s):  
Aisyah Mohd Ismail ◽  
Farida Zuraina Mohd Yusof

Random Amplified Polymorphic DNA (RAPD) applies single arbitrary short primers (8-12nucleotides) to produce many amplified discrete DNA. Limited reports and studies were done onthe use of long primers (over 12 bases). This study was performed to investigate the potential valueof long primers (15-21 bases) for generating RAPD polymorphisms. We compared both short andlong primers in RAPD assays of two date palm cultivars grown in Malaysia: Ajwa and Barhi. Thenumber of produced polymorphic fragments ranged in order from 2 and 38 bands for short andlong primers in Ajwa. Meanwhile, more polymorphic fragments were generated by long primersin Barhi, which were 50 and only five bands for short primers. 18-mer GY107 and 20-mer CO4primers yielded 100% polymorphism in Ajwa and Barhi, respectively. Moreover, long primersproduced more DNA fragments and a wider range of DNA fragment sizes (from 140-1600 bp,with respect to 300-1000 bp obtained with 10-mer primers). Hence, a significant correlation wasobserved between primer length and the number of polymorphic fragments within the long primergroup, suggesting that increasing primer length above 15 bases may demonstrate enhancedproduction of more polymorphism.


2021 ◽  
pp. 2108479
Author(s):  
Fatemeh Farhangdoust ◽  
Feng Cheng ◽  
Wentao Liang ◽  
Yongmin Liu ◽  
Meni Wanunu

Author(s):  
Shuangying Jiang ◽  
Yuanwei Tang ◽  
Liang Xiang ◽  
Xinlu Zhu ◽  
Zelin Cai ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Maria Pallarès-Masmitjà ◽  
Dimitrije Ivančić ◽  
Júlia Mir-Pedrol ◽  
Jessica Jaraba-Wallace ◽  
Tommaso Tagliani ◽  
...  

AbstractWhile multiple technologies for small allele genome editing exist, robust technologies for targeted integration of large DNA fragments in mammalian genomes are still missing. Here we develop a gene delivery tool (FiCAT) combining the precision of a CRISPR-Cas9 (find module), and the payload transfer efficiency of an engineered piggyBac transposase (cut-and-transfer module). FiCAT combines the functionality of Cas9 DNA scanning and targeting DNA, with piggyBac donor DNA processing and transfer capacity. PiggyBac functional domains are engineered providing increased on-target integration while reducing off-target events. We demonstrate efficient delivery and programmable insertion of small and large payloads in cellulo (human (Hek293T, K-562) and mouse (C2C12)) and in vivo in mouse liver. Finally, we evolve more efficient versions of FiCAT by generating a targeted diversity of 394,000 variants and undergoing 4 rounds of evolution. In this work, we develop a precise and efficient targeted insertion of multi kilobase DNA fragments in mammalian genomes.


2021 ◽  
Author(s):  
Vesna Bacheva ◽  
Federico Paratore ◽  
Maya Dolev ◽  
Baruch Rofman ◽  
Govind Kaigala ◽  
...  

We present a microfluidic device for selective separation and extraction of molecules based on their diffusivity. The separation relies on electroosmotically-driven bidirectional flows in which high diffusivity species experience a net-zero velocity, and lower diffusivity species are advected to a collection reservoir. The device can operate continuously and is suitable for processing low sample volumes. Using several model systems, we showed that the extraction efficiency of the system is maintained at more than 90% over tens of minutes, with a purity of more than 99%. We demonstrate the applicability of the device to the extraction of genomic DNA from short DNA fragments.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fred Russell Kramer ◽  
Diana Yaneth Vargas

AbstractSuperSelective primers, by virtue of their unique design, enable the selective exponential amplification of rare DNA fragments containing somatic mutations in the presence of abundant closely related wild-type DNA fragments. However, when a SuperSelective primer is used in conjunction with a conventional reverse primer, linear amplification of the abundant wild-type fragments occurs, and this may lead to a late arising signal that can be confused with the late arising signal from the rare mutant fragments. We have discovered that the use of a pair of SuperSelective primers, one specific for the target mutation in a plus strand, and the other specific for the same mutation in the complementary minus strand, but both possessing 3′-terminal nucleotides that are complementary to the mutation, significantly suppresses the linear amplification of the related wild-type sequence, and prevents the generation of false mutant sequences due to mis-incorporation by the DNA polymerase. As a consequence, the absence of mutant fragments in a sample does not give rise to a false-positive signal, and the presence of mutant fragments in a sample is clearly distinguishable as a true-positive signal. The use of SuperSelective primer pairs should enhance the sensitivity of multiplex PCR assays that identify and quantitate somatic mutations in liquid biopsies obtained from patients with cancer, thereby enabling the choice of a targeted therapy, the determination of its effectiveness over time, and the substitution of a more appropriate therapy as new mutations arise.


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