SNP Analysis Using a Molecular Beacon-Based Operating Cooperatively (OC) Sensor

2013 ◽  
pp. 81-86 ◽  
Author(s):  
Evan M. Cornett ◽  
Dmitry M. Kolpashchikov
Keyword(s):  
Molecular Beacon ◽  
Snp Analysis

scholarly journals Molecular-Beacon-Based Tricomponent Probe for SNP Analysis in Folded Nucleic Acids

2011 ◽  
Vol 17 (46) ◽  
pp. 13052-13058 ◽  
Author(s):  
Camha Nguyen ◽  
Jeffrey Grimes ◽  
Yulia V. Gerasimova ◽  
Dmitry M. Kolpashchikov
Keyword(s):  
Nucleic Acids ◽  
Molecular Beacon ◽  
Snp Analysis

Genetic polymorphisms as the predictors of response to antiviral treatment in chronic hepatitis C virus infection

2011 ◽  
Vol 152 (22) ◽  
pp. 876-881
Author(s):  
Alajos Pár
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Genetic Polymorphisms ◽  
Chronic Hepatitis C ◽  
Genome Wide Association Study ◽  
Antiviral Treatment ◽  
Hcv Infection ◽  
Snp Analysis ◽  
Chronic Hcv

The review discusses the genetic polymorphisms involved in the pathogenesis of hepatitis C virus (HCV) infection, that may determine the outcome of disease. In this field earlier both certain major histocompatibility complex (MHC) alleles and some cytokine gene variants have also been studied. Recently, the genome-wide association study (GWAS) and targeted single nucleotide polymorphism (SNP) analysis have revealed that a variant in the promoter region of interleukin-28B (IL-28B) gene is strongly linked to viral clearance and it may be the strongest pretreatment predictor of treatment response in chronic hepatitis C. Last year it was shown that two genetic variants leading to inosine triphosphatase deficiency protect against haemolytic anemia in patients receiving ribavirin during antiviral treatment for chronic HCV infection. Orv. Hetil., 2011, 152, 876–881.

scholarly journals Single Step In Situ Detection of Surface Protein and MicroRNA in Clustered Extracellular Vesicles Using Flow Cytometry

2021 ◽  
Vol 10 (2) ◽  
pp. 319
Author(s):  
Hee Cheol Yang ◽  
Won Jong Rhee
Keyword(s):  
Extracellular Vesicles ◽  
Liquid Biopsy ◽  
Molecular Beacon ◽  
Disease Diagnosis ◽  
Single Step ◽  
Flow Cytometer ◽  
Surface Proteins ◽  
Biomarker Detection ◽  
In Situ Detection

Because cancers are heterogeneous, it is evident that multiplexed detection is required to achieve disease diagnosis with high accuracy and specificity. Extracellular vesicles (EVs) have been a subject of great interest as sources of novel biomarkers for cancer liquid biopsy. However, EVs are nano-sized particles that are difficult to handle; thus, it is necessary to develop a method that enables efficient and straightforward EV biomarker detection. In the present study, we developed a method for single step in situ detection of EV surface proteins and inner miRNAs simultaneously using a flow cytometer. CD63 antibody and molecular beacon-21 were investigated for multiplexed biomarker detection in normal and cancer EVs. A phospholipid-polymer-phospholipid conjugate was introduced to induce clustering of the EVs analyzed using nanoparticle tracking analysis, which enhanced the detection signals. As a result, the method could detect and distinguish cancer cell-derived EVs using a flow cytometer. Thus, single step in situ detection of multiple EV biomarkers using a flow cytometer can be applied as a simple, labor- and time-saving, non-invasive liquid biopsy for the diagnosis of various diseases, including cancer.

Genome-wide SNP analysis suggests male heterogamety in bighead catfish (Clarias macrocephalus, )

Aquaculture ◽  
2021 ◽  
pp. 737005
Author(s):  
Dung Ho My Nguyen ◽  
Jatupong Ponjarat ◽  
Nararat Laopichienpong ◽  
Ekaphan Kraichak ◽  
Thitipong Panthum ◽  
...  
Keyword(s):  
Snp Analysis ◽  
Genome Wide ◽  
Clarias Macrocephalus ◽  
Male Heterogamety

scholarly journals The seasonal changes of the gut microbiome of the population living in traditional lifestyles are represented by characteristic species-level and functional-level SNP enrichment patterns

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xue Zhu ◽  
Jiyue Qin ◽  
Chongyang Tan ◽  
Kang Ning
Keyword(s):  
Gut Microbiome ◽  
Seasonal Changes ◽  
Dry Season ◽  
Urban Setting ◽  
Snp Analysis ◽  
Wet Season ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Genome Level ◽  
Prevalent Species

Abstract Background Most studies investigating human gut microbiome dynamics are conducted on humans living in an urban setting. However, few studies have researched the gut microbiome of the populations living traditional lifestyles. These understudied populations are arguably better subjects in answering human-gut microbiome evolution because of their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have exhibited high biodiversity and seasonal patterns in their gut microbiome composition at the family level, where some taxa disappear in one season and reappear later. Such seasonal changes have been profiled, but the nucleotide changes remain unexplored at the genome level. Thus, it is still elusive how microbial communities change with seasonal changes at the genome level. Results In this study, we performed a strain-level single nucleotide polymorphism (SNP) analysis on 40 Hadza fecal metagenome samples spanning three seasons. With more SNP presented in the wet season, eight prevalent species have significant SNP enrichment with the increasing number of SNP calling by VarScan2, among which only three species have relatively high abundances. Eighty-three genes have the most SNP distributions between the wet season and dry season. Many of these genes are derived from Ruminococcus obeum, and mainly participated in metabolic pathways including carbon metabolism, pyruvate metabolism, and glycolysis. Conclusions Eight prevalent species have significant SNP enrichments with the increasing number of SNP, among which only Eubacterium biforme, Eubacterium hallii and Ruminococcus obeum have relatively high species abundances. Many genes in the microbiomes also presented characteristic SNP distributions between the wet season and the dry season. This implies that the seasonal changes might indirectly impact the mutation patterns for specific species and functions for the gut microbiome of the population that lives in traditional lifestyles through changing the diet in wet and dry seasons, indicating the role of these variants in these species’ adaptation to the changing environment and diets.

scholarly journals Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 201
Author(s):  
Sang Mee Hwang ◽  
Hee Won Cho ◽  
Tae Yeul Kim ◽  
Jeong Su Park ◽  
Jongtak Jung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Snp Analysis ◽  
Whole Genome ◽  
Phylogenetic Tree Analysis ◽  
Web Based ◽  
Hospital Outbreak ◽  
Carbapenem Resistant ◽  
Bioinformatics Tools

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

scholarly journals Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

2021 ◽  
Author(s):  
Noemi Bellassai ◽  
Roberta D’Agata ◽  
Giuseppe Spoto
Keyword(s):  
Nucleic Acid ◽  
Structural Properties ◽  
Molecular Beacon ◽  
Dna Origami ◽  
Molecular Beacons ◽  
Conformational Polymorphism ◽  
Functional Systems ◽  
Similarities And Differences ◽  
Nucleic Acid Structures ◽  
Nucleic Acid Sequences

AbstractNucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

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