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.
Authors:Reza Ranjbar, Payam Behzadi, and Shohreh Farshad
Helicobacter pylori is a Gram-negative motile bacterium causative agent of acute and chronic digestive and extra-digestive human infections. According to different reports worldwide, H. pylori symptomatic and asymptomatic infections are a global problem. The statistical investigations show a percentage of 50 for people who are involved in H. pylori acute/chronic digestive and/or extra-digestive infections around the world. This review focuses on digestive and extra-digestive diseases caused by H. pylori, the related virulence factors, diagnostic techniques including non-invasive and invasive diagnostics and treatment. There is an abundance of diagnostics for detection and identification of H. pylori. The availability, cost, and the condition of test performance may differ from place to place. To increase the level of reliability in association with diagnostic tools for detecting H. pylori, several techniques must be applied at once as multi-diagnostic technique. Furthermore, there are several pharmacotherapies which can be used for complete eradication of H. pylori infection.
Authors:Reza Ranjbar, Masomeh Bolandian, and Payam Behzadi
Shigellosis is a considerable infectious disease with high morbidity and mortality among children worldwide. In this survey the prevalence of four important virulence genes including ial, ipaH, set1A, and set1B were investigated among Shigella strains and the related gene profiles identified in the present investigation, stool specimens were collected from children who were referred to two hospitals in Tehran, Iran. The samples were collected during 3 years (2008–2010) from children who were suspected to shigellosis. Shigella spp. were identified throughout microbiological and serological tests and then subjected to PCR for virulotyping. Shigella sonnei was ranking first (65.5%) followed by Shigella flexneri (25.9%), Shigella boydii (6.9%), and Shigella dysenteriae (1.7%). The ial gene was the most frequent virulence gene among isolated bacterial strains and was followed by ipaH, set1B, and set1A. S. flexneri possessed all of the studied virulence genes (ial 65.51%, ipaH 58.62%, set1A 12.07%, and set1B 22.41%). Moreover, the pattern of virulence gene profiles including ial, ial–ipaH, ial–ipaH–set1B, and ial–ipaH–set1B–set1A was identified for isolated Shigella spp. strains. The pattern of virulence genes is changed in isolated strains of Shigella in this study. So, the ial gene is placed first and the ipaH in second.
Authors:Payam Behzadi, Elham Behzadi, and Reza Ranjbar
Among a wide range of cytokines, the Interleukin 12 (IL-12) family has its unique structural, functional, and immunological characteristics that have made this family as important immunological playmakers. Because of the importance of IL-12 heterodimeric cytokines in microbial infections, autoimmune diseases, and cancers, the authors of this literature discuss about the general characteristics of IL-12 family members, the interactions between IL-12 cytokines and pathogenic microorganisms, the interleukins receptors and their strategies for selecting different signalling pathways. IL-12 and IL-23 are similar in p40 subunits and both are involved in proinflammatory responses while, IL-27 and IL-35 contribute to anti-inflammatory activities; however, IL-27 is also involved in pro-inflammatory responses. There are some similarities and dissimilarities among IL-12 family members which make them a unique bridge between innate and adaptive immune systems. The bioactivities of IL-12 family indicate a brilliant promise for their applications in different fields of medicine. The members of IL-12 family are candidate for several therapeutics including gene therapy, cancer therapy, tumour therapy, and vaccination. To have an accurate diagnostic technique and definite treatment regarding to infectious diseases, the playmakers of IL-12 family as effective criteria together with microarray technology are the best choices for current and future applications.
Authors:Reza Ranjbar, Ali Naghoni, Shohreh Farshad, Hadi Lashini, Ali Najafi, Nourkhoda Sadeghifard, and Caterina Mammina
We evaluated the performances of a newly designed real-time polymerase chain reaction (PCR) assay using TaqMan® probes to detect Salmonella Typhi. TaqMan® real-time PCR assays were performed by designed primers and probe based on the staG gene for detecting S. Typhi. The specificity of the assay was evaluated on 15 Salmonella serovars. The analytical specificity was evaluated on 20 non-Salmonella microorganisms. The analytical sensitivity was assessed using decreasing DNA quantities of S. Typhi ATCC 19430. Finally the detection capability of the TaqMan® real-time PCR assay on isolates recovered from patients with Salmonella infections was compared to the conventional PCR assay. Only S. Typhi strain had positive results when subjected to the assay using Typhi-specific real-time PCR. No amplification products were observed in real-time PCR with any of the non-Salmonella microorganisms tested. The TaqMan® real-time PCR was more sensitive than the conventional PCR. In conclusion, we found that the easy-to-use real-time PCR assays were faster than conventional PCR systems. The staG-based TaqMan® real-time PCR assay showed to be specific and sensitive method for the safe and rapid detection of the S. Typhi.
Authors:Negin Khomarlou, Parviz Aberoomand-Azar, Ardalan Pasdaran Lashgari, Hamid Tebyanian, Ali Hakakian, Reza Ranjbar, and Seyed Abdolmajid Ayatollahi
The objective of this study was to identify the bioactive compounds of essential oil and evaluate the antibacterial activity of the essential oil extracted from Chenopodium album subsp. striatum against multidrug-resistant bacterial strains (MDR) which were isolated from clinical specimens by conventional methods. Furthermore, eight different Gram-negative and Gram-positive multidrug-resistant bacterial strains were used to investigate the antibacterial potential of the essential oil. The antibacterial activity was tested using MIC and MBC microdilution method, well and disc diffusion in different concentration. The hydro-distillation of aerial parts powder yield was 0.466% (v/w). Essential oil showed bactericidal activity against both MDR Gram-negative and Gram-positive bacterial strains. MIC and MBC results were ranged from 0.31 to 2.5 and 0.62 to 5.0 mg/mL. The inhibition zones in well-diffusion method were ranged from 7 ± 0.6 mm to 15 ± 1.0 mm. Disc diffusion method was ranged from 7 ± 0.0 mm to 16 ± 0.6 mm depending on the type of bacteria strain and essential oil concentration. Essential oil of Ch. album had the greatest potential to be considered as an antibacterial agent against MDR bacteria strain. This potential was due to different biological and bioactive compounds like phytol, linalool, α-terpineol and linolenic acid in the plant.