مقالات رزومه فاطمه شیخی

Bacterial food poisoning is considered a global concern in terms of economical and human health. Staphylococcus aureus produces low molecular weight extracellular toxins. These enterotoxins (SEs) are similar in structure and bioactivity. Today, there are several methods to detect SE genes. Nevertheless, culture-based and immunological methods are simple and cheaper than molecular techniques, they are time-consuming, with low sensitivity and specificity. In this field, loop-mediated isothermal amplification (LAMP) is a fast and simple method for gene amplification. The aim of this work was to optimize the LAMP reaction using the Taguchi method. For this, in order to improve and accelerate the LAMP diagnostic process, essential factors for the identification of enterotoxin, including MgSO4 concentration, time, and temperature reaction were optimized separately and using Taguchi experimental design. The results showed that 57 µg/ml of S. aureus genome as template is suitable for the replication, and in optimization of LAMP assay in separate condition the best replication rate was observed at 6 mM MgSO4, 45 min, and 65 °C. Whereas using Taguchi methods, the optimum condition was at 8 mM MgSO4, 60 min and 65 °C. The one-step-visual developed LAMP assay with the optimum conditions could be of interest for screening functions in food analytical laboratories, and a portable detection method could be used to design a suitable identification kit for S. aureus without the need for special equipment or trained personnel.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has currently caused a significant pandemic among worldwide populations. The high transmission and mortality rates of the disease necessitate studies for rapid designing and effective vaccine production. This study aims to predict and design a novel multi-epitope vaccine against the SARS-CoV-2 virus using bioinformatics approaches. 

Coronavirus envelope proteins, Open Reading Frame 7b (ORF7b), Open Reading Frame 8 (ORF8), Open Reading Frame 10 (ORF10), and Nonstructural protein 9 (Nsp9) were selected as targets for epitope mapping using Immune Epitope Data Bank (IEDB) and BepiPred 2.0 servers. Also, molecular docking studies were performed to determine the candidate vaccine’s affinity to Toll-Like Receptor (TLR3, TLR4) and Major Histocompatibility Complex (MHC I and MHC II) molecules. Thirteen epitopes were selected to construct the multi-epitope vaccine. 

We found that the constructed peptide has valuable antigenicity, stability, and appropriate half-life. The Ramachandran and ERRAT plots approved the quality of the predicted model after the refinement process. Molecular docking investigations revealed that antibody-mode in the ClusPro 2.0 server showed the lowest binding energy for MHC I, MHC II, TLR3, and TLR4.

The designed vaccine has a good antigenicity and stability and could be a proper vaccine candidate against the Coronavirus Disease 2019 (COVID-19) infectious disease though, in vitro and in vivo experiments are necessary to complete and confirm our results.

Yersinia pestis and Francisella tularensis cause plague and tularemia, which are known as diseases of the newborn and elderly, respectively. Immunological and culture-based detection methods of these bacteria are time-consuming, costly, complicated and require advanced equipment. We aimed to design and synthesize a gene structure as positive control for molecular detection of these bacteria.
Conserved regions of each bacterium were determined. A fragment containing the fopA and caf1 genes (conserved genes of F. tularensis and Y. pestis, respectively) was artificially synthesized, cloned into the pUC57 vector (pUC-fopA-caf1), transformed into E. coli DH5α, and used in a multiplex PCR assay. The sensitivity of this assay was examined by serial dilution of the extracted plasmid, whereas the specificity was examined using genomes of Escherichia coli, Salmonella typhi, Enterobacter aerogenes, Vibrio cholerae as templates. Finally, PCR products were analyzed in agarose gel electrophoresis.
As expected, our analysis showed a clear dual band in the size range of 107 bp to 176 bp, confirming the presence of fopA and caf1 genes. Another 351 bp band was detected due to amplification being dependent on the forward primer of fopA and the reverse primer of caf1. Optimization of the PCR protocol reduced the amplification of this 351 bp band. The sensitivity of this assay was determined to be 36×10 -3 ng/µl and the selectivity test confirmed the specificity of this method is appropriate for the detection of target genes.
This multiplex PCR method could be used in research laboratories for identification of these important pathogens.