Nucleic Acid-Based Approaches for Detection of Viral Hepatitis

Behzadi, Payam; Ranjbar, Reza; Alavian, Seyed Moayed

doi:10.5812/jjm.17449

Cited by 29 publications

(26 citation statements)

References 48 publications

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“…They also are cost effective; but, they are not accurate, sensitive, specific and cost effective in the cases with huge number of specimens [16, 17, 21, 24, 25, 36, 41, 43, 46]. …”

Section: Discussionmentioning

confidence: 99%

Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

2016

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Background: Francisella tularensis (F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.Objective:The main goal of this original article was to design suitable long oligo microarray probes for detection and identification of F. tularensis.Method:For performing this research, the complete genomes of F. tularensis subsp. tularensis FSC198, F. tularensis subsp. holarctica LVS, F. tularensis subsp. mediasiatica, F. tularensis subsp. novicida (F. novicida U112), and F. philomiragia subsp. philomiragia ATCC 25017 were studied via NCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processed via AlleleID 7.7 software and Oligoanalyzer tool, respectively.Results:In this in silico investigation, a number of long oligo microarray probes were designed for detecting and identifying F. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.Conclusion:Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.

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“…They also are cost effective; but, they are not accurate, sensitive, specific and cost effective in the cases with huge number of specimens [16, 17, 21, 24, 25, 36, 41, 43, 46]. …”

Section: Discussionmentioning

confidence: 99%

Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

2016

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“…Microarray technology is divided into three types of DNA, protein and RNA microarray tools. The outcome of microarray technology is reliable, sensitive, specific, flexible and rapid with high accuracy [4,7,8,[87][88][89][90][91][92][93].…”

Section: Diagnostic Methods For Virulence Genes Of Filamentous Adhesinsmentioning

confidence: 99%

Uropathogenic Escherichia coli and Fimbrial Adhesins Virulome

Behzadi¹

2018

Urinary Tract Infection - The Result of the Strength of the Pathogen, or the Weakness of the Host

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Urinary tract infections (UTIs) rank second among infectious diseases around the world, and this makes them significant. There are many microbial agents which may cause UTIs. Enterobacteriaceae family members are recognized as important UTI bacterial causative agents. Among them, uropathogenic Escherichia coli (UPEC) pathotypes are considered as the most important bacterial agents of UTIs. Today, genomics and bioinformatics explain us why UPEC strains are so considerable pathogens regarding UTIs. There is a diversity of E. coli strains involving commensal and pathogenic strains. Genomics shows that commensal strains of E. coli encompass the minimal amount of genome and genetic elements among E. coli populations, whereas the pathotypes of E. coli possess the maximal or a big portion of genomic elements. Previous studies confirm the presence of a vast range of virulence genes within the pool of E. coli pathotypes like UPEC. So, the pool of virulence genes (virulome) belonging to UPEC enables UPEC pathotypes to have huge genomes with the ability of different levels of pathogenesis. The more virulence factors, the more pathogenicity. Due to the presence of a mass of virulence factors within UPEC cellular structures, well-known fimbrial adhesins in UPEC pathotypes are discussed in this chapter.

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“…The probe designing section is known as an in silico procedure that should be performed in dry lab, whereas the wet lab section of the technology (probe spotting, target labeling, hybridization, and scanning) involves the in vitro portion. The unique characteristics of microarray includes the immobilization of specific designed probes as anchored sequences on a solid and coated chip to analyze a genome, a proteome, or a transcriptome among a huge number of samples and specimens [1,3,4,[16][17][18][19][20][21][22][23].…”

Section: Dna Microarray Characteristicsmentioning

confidence: 99%

DNA microarray technology and bioinformatic web services

Behzadi

Ranjbar

2018

AMicr

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The pan-genomic microarray technique is used for environmental and/or clinical studies. Although microarray is an accurate and sharp diagnostic tool, the expertized bioinformaticians were able to minimize the outcome biases and maximize the flexibility and accuracy of the technique. The knowledge of bioinformatics plays a key role in association with probe designing and the utilization of correct probe sets and platforms. This technique is divided into two parts as dry lab (in silico studies) and wet lab (in vitro studies). Each part covers the other and are known as complementary divisions. In the case of microarray probe designing, a wide range of software, tools, and databases are necessary. Obviously, the application of right databases, software, and tools decreases the probable biases in the outcomes. Due to the importance of suitable probe designing, this article has focused its look onto a variety of online/offline databases, software, and tools.

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Nucleic Acid-Based Approaches for Detection of Viral Hepatitis

Cited by 29 publications

References 48 publications

Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

Uropathogenic Escherichia coli and Fimbrial Adhesins Virulome

DNA microarray technology and bioinformatic web services

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