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Meysam Sarshar

Università degli Studi "La Sapienza" di Roma, Department of Pubblic Health and Infectious Diseases, Graduate Student

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Meysam Sarshar received his Ph.D in Infectious diseases and Microbiology from Sapienza University of Rome, Italy in 2018. His most recent publication is "Acinetobacter baumannii Targets Human Carcinoembryonic Antigen-Related Cell Adhesion Molecules (CEACAMs) for Invasion of Pneumocytes". Research interests: host-pathogen interactions, intestinal and extraintestinal E. coli, urinary tract infections, bacterial virulence factors, bacterial adhesion, invasion and persistence, antibiotic resistance mechanisms, and Fecal miRNA.
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Papers by Meysam Sarshar

Adaptive strategies of uropathogenic Escherichia coli CFT073: from growth in lab media to virulence during host cell adhesion

International Microbiology, 2022

Urinary tract infections (UTIs) are a major concern in public health. The prevalent uropathogenic... more Urinary tract infections (UTIs) are a major concern in public health. The prevalent uropathogenic bacterium in healthcare settings is Escherichia coli. The increasing rate of antibiotic-resistant strains demands studies to understand E. coli pathogenesis to drive the development of new therapeutic approaches. This study compared the gene expression profile of selected target genes in the prototype uropathogenic E. coli (UPEC) strain CFT073 grown in Luria Bertani (LB), artificial urine (AU), and during adhesion to host bladder cells by semi-quantitative real-time PCR (RT-PCR) assays. AU effectively supported the growth of strain CFT073 as well as other E. coli strains with different lifestyles, thereby confirming the appropriateness of this medium for in vitro models. Unexpectedly, gene expression of strain CFT073 in LB and AU was quite similar; conversely, during the adhesion assay, adhesins and porins were upregulated, while key global regulators were downregulated with respect to lab media. Interestingly, fimH and papGII genes were significantly expressed in all tested conditions. Taken together, these results provide for the first time insights of the metabolic and pathogenic profile of strain CFT073 during the essential phase of host cell adhesion.

Inflammatory Response in Caco-2 Cells Stimulated with Anisakis Messengers of Pathogenicity

by Ilaria Bellini and Meysam Sarshar

Pathogens, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more

Optimization of 3D islet-like cluster derived from human pluripotent stem cells: An efficient in vitro differentiation protocol

by Meysam Sarshar and S. Ghorbani-dalini

Gene, 2022

Development of an optimized protocol to produce sufficient functional human insulin-producing isl... more Development of an optimized protocol to produce sufficient functional human insulin-producing islet-like cluster is important as a potential therapeutic strategy for diabetes as well as in vitro studies. Here, we described a stepwise protocol for differentiation of the human induced pluripotent stem cell line (R1-hiPSC1) into the isletlike cluster using several growth factors and small molecules. Therefore, various differentiation steps have been adopted to maximize mimicking of developmental processes in order to form functional islet like cluster. The differentiation protocol enables us to generate 3D islet-like clusters with highly viable cells, which are insulin producer and glucose responsive. Transcriptome analysis of transcription factors and functional genes revealed high coordination between gene expressions and resembling to those reported during natural development of islet cell. This coordination was further confirmed by hierarchical clustering of genes during differentiation. Furthermore, the islet-like clusters were enriched with insulin producing cells and formed glucose responsiveness behavior upon stimulation with glucose. Our protocol provides a robust platform and well-behaved model for additional developmental studies and shed light our clusters as a good candidate for in vitro model. Further studies are needed to assess the hormonal content of this cluster as well as transplantation into the animal model.

The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions

Frontiers in Molecular Biosciences, 2022

Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances i... more Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein–RNA and RNA–RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.

Insightful Improvement in the Design of Potent Uropathogenic E. coli FimH Antagonists

Pharmaceutics , 2023

This article is an open access article distributed under the terms and conditions of the Creative... more

The Interleukin-1 (IL-1) Superfamily Cytokines and Their Single Nucleotide Polymorphisms (SNPs)

Journal of Immunology Research

Interleukins (ILs)—which are important members of cytokines—consist of a vast group of molecules,... more Interleukins (ILs)—which are important members of cytokines—consist of a vast group of molecules, including a wide range of immune mediators that contribute to the immunological responses of many cells and tissues. ILs are immune-glycoproteins, which directly contribute to the growth, activation, adhesion, differentiation, migration, proliferation, and maturation of immune cells; and subsequently, they are involved in the pro and anti-inflammatory responses of the body, by their interaction with a wide range of receptors. Due to the importance of immune system in different organisms, the genes belonging to immune elements, such as ILs, have been studied vigorously. The results of recent investigations showed that the genes pertaining to the immune system undergo progressive evolution with a constant rate. The occurrence of any mutation or polymorphism in IL genes may result in substantial changes in their biology and function and may be associated with a wide range of diseases and d...

Biomarkers to Monitor Adherence to Gluten-Free Diet by Celiac Disease Patients: Gluten Immunogenic Peptides and Urinary miRNAs

Foods

Celiac disease (CD) is a multifactorial autoimmune enteropathy with a prevalence greater than 1% ... more Celiac disease (CD) is a multifactorial autoimmune enteropathy with a prevalence greater than 1% in the pediatric population. The only therapy for CD patients is a strict gluten-free diet (GFD). Gluten-free food contamination by other cereals during packaging and cooking or accidental ingestion of gluten may cause several intestinal and extraintestinal symptoms in CD patients. Therefore, the monitoring of gluten contamination in food and assessing the level of ingested gluten by analytical biomarkers has been of great interest in recent years. To this aim, small gluten immunogenic peptides (GIPs) obtained by the hydrolysis of gluten and present in urine and feces have been studied as biomarkers of gluten intake and to monitor adherence to GFD by CD patients. More recently, the use of circulating, fecal and urinary miRNAs has emerged as a novel diagnostic tool that can be potentially applied to assess adherence to GFD. Moreover, the presence of GIPs and miRNAs in both feces and urine...

Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach

International Journal of Molecular Sciences, 2019

Carbapenem-resistant Acinetobacter baumannii strains cause life-threatening infections due to the... more Carbapenem-resistant Acinetobacter baumannii strains cause life-threatening infections due to the lack of therapeutic options. Although the main mechanisms underlying antibiotic-resistance have been extensively studied, the general response to maintain bacterial viability under antibiotic exposure deserves to be fully investigated. Since the periplasmic space contains several proteins with crucial cellular functions, besides carbapenemases, we decided to study the periplasmic proteome of the multidrug-resistant (MDR) A. baumannii AB5075 strain, grown in the absence and presence of imipenem (IMP). Through the proteomic approach, 65 unique periplasmic proteins common in both growth conditions were identified: eight proteins involved in protein fate, response to oxidative stress, energy metabolism, antibiotic-resistance, were differentially expressed. Among them, ABUW_1746 and ABUW_2363 gene products presented the tetratricopeptide repeat motif, mediating protein-protein interactions. ...

Microbiota-Derived Extracellular Vesicles as New Systemic Regulators

Frontiers in Microbiology, 2017

Genetic diversity of clinical strains of Salmonella enterica serovar Typhimurium

Journal Mil Med, Jul 15, 2012

Aims: Salmonella spp. is one of the most common pathogenic bacteria responsible for gastroenterit... more Aims: Salmonella spp. is one of the most common pathogenic bacteria responsible for gastroenteritis in human. Among Salmonella spp., S. typhimurium has many hosts other than humans and its prevalence rate is high in society. The aim of this study was to determine the ribotype diversity of S. typhimurium stains isolated in some hospitals of Tehran, Iran. Methods: In this descriptive study, clinical samples were collected from different hospitals in Tehran were investigated. Bacterial isolation was carried out by standard procedures in selective culture media and identification was achieved through biochemical and serological methods. DNA extraction was performed by phenol-cholorophorm methods. Ribotyping was used for molecular typing of S. typhimurium clinical isolates. Results: The sizes of the ribotyping bands ranged from 1.4 to 16.8 kb in all ribotypes. The S. typhimurium isolates were divided into 7 clusters based on the diversity of ribosomal genome areas. Most isolates (5 strains) belonged to the cluster 2b. Three isolates belonged to the 6b cluster and for the rest of isolates, each belhonged to one of other clusters. Conclusion: S. typhimurium strains circulating in the studied hospitals of Tehran, do not belong to a specific ribotype and have ribotype diversity, but other molecular typing methods should be implemented in order to make a more precise judjement about the presence of whether limited or widespread clones and the relationship among the different strains of this serotype.

The Phylum Spirochaetaceae

Evaluation of OipA and DupA Genes in Helicobacter Pylori Strains and Their Relationship with Different Gastroduodenal Diseases

Abstract Background and Objectives: Helicobacter pylori cause gastroduodenal diseases. Studies su... more

Outer membrane vesicles are the powerful cell-to-cell communication vehicles that allow bacteria to monitor extracellular milieu

ExRNA

Existence of cell-to-cell communication strategies among bacteria (i.e., defined as inter-species... more Existence of cell-to-cell communication strategies among bacteria (i.e., defined as inter-species, intra-species, and inter-kingdom crosstalk) reveals how genius they are (1,2). The common and well-studied language for bacterial communication is quorum sensing (QS), an informative signaling pathway within a bacterial population (3-5). Specifically, bacteria secrete signaling modules under QS regulation, known as autoinducers (AIs), to share quorum information and regulate group behaviours. QS modulates the expression of bacterial pathogenicity factors involved in the infection process, as a similar regulation could occur in the physiology of host cells. Detailed mechanisms are extensively reviewed (6,7). Bacterial conversation enables them to feel the surrounding stimuli and coordinate their gene expression accordingly. This cooperation in sensing and responding to environmental changes could result in arrays of behaviour, ranging from symbiosis to virulence, biofilm formation, stress adaptation and natural product production, leading bacteria to live like multicellular organisms (8-10). Furthermore, bacteria need to manage competition for ecological niches and resources that favour their survival and genetic persistence. This strategy underlies mechanisms of complex interactions that occur among bacteria as well as bacteria-hosts. While the potency of QS has gained the interest of researchers for a long time, only recently QS-regulated pathways have been reported to be involved in membrane vesicles (MVs) or outer membrane vesicles (OMVs) biogenesis in Gram-positive and Gram-negative bacteria, respectively (11). OMVs have been recognized as an alternative vehicle for cell-to-cell signaling in bacteria. This spherical membranous structure can package cargoes such as virulence factors, biologically active proteins, DNA, RNA, as well as signaling molecules, playing an important role in bacterial adaptation and survival (2,12). Despite tremendous progress in the OMVs field (e.g., involvement in disease-related processes and delivery mechanisms into host cells), there is still some uncertainty in the biogenesis of OMVs and their precise sorting mechanisms within bacterial communities. So far, there is enough evidence connecting QS and OMVs, indicating that either QS molecules could serve as OMVs cargo or they are able to control the release of OMVs in several nosocomial pathogens (i.e., Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii and Escherichia coli) (13). The latter mechanism could act either by stimulating OMVs secretion, a phenomenon evidenced in P. aeruginosa, Vibrio harveyi, Stenotrophomonas maltophilia, as well as in plant pathogens such as Xanthomonas oryzae and Xanthomonas campestris or vice versa by inhibiting its release as reported in Xylella fastidiosa (14-18). For instance, through a QS-regulated process, OMVs released by the environmental pathogen Chromobacterium

Genotyping of Salmonella Enterica Serovar Enteritidis Strains Isolated from Clinical Samples by Pulsed-Field Gel Electrophoresis (PFGE)

مجله دانشکده پزشکی اصفهان, 2013

Background: The infections caused by Salmonella enterica serovar enteritidis (Salmonella enteriti... more Background: The infections caused by Salmonella enterica serovar enteritidis (Salmonella enteritidis) have been increasing in developed and developing countries. The aim of this study was to investigate the genetic relationship between the strains of Salmonella enteritidis. Methods: In a descriptive study from 2008 to 2010, clinical Salmonella enteritidis strains were collected from the patients referred to different hospitals in Tehran. The strains identified by biochemical and serological methods. Genetic relationships between the isolates were investigated using pulsed field gel electrophoresis (PFGE) method. Findings: Of 40 Salmonella enteritidis isolated strains, two PFGE profiles were obtained which among them, 32 (80%) and 8 (20%) of isolates belonged to cluster A and cluster B, respectively. Based on PFGE patterns, 28 (70%) strains exhibited nine bands and were belonged to cluster A. Conclusion: The result of this study indicated that isolated Salmonella enteritidis strains ...

The study of the oipA and dupA genes in Helicobacter pylori strains and their relationship with different gastroduodenal diseases

Aim: The purpose of this investigation was to determine the oipA and dupA genes of Helicobacter p... more Aim: The purpose of this investigation was to determine the oipA and dupA genes of Helicobacter pylori isolates from west of Iran; Chaharmahalo Bakhtiyari region and find their relationship with the severity of the gastroduodenal diseases. Background: Helicobacter pylori is an organism responsible for many gastroduodenal diseases. Many studies suggest that genetic diversity in H. pylori virulence factors such as oipA and dupA genes is high among isolates of different geographic regions and may cause more severe diseases. Patients and methods: In this cross-sectional study, gastric biopsy specimens were taken from 150 patients suffering from gastroduodenal diseases. The presence of ureC, dupA and oipA genes was tested by polymerase chain reaction (PCR). Results: Overall, 123 (82%) H. pylori strains were isolated from 150 specimens. dupA gene was detected in 41 (33.33%) H.pylori-positive specimens. There was a reverse correlation between this gene and gastric cancer. The oipA gene was...

Protective Effect of HLA-E*0101/*0103 Genotype in Survival of Patients After Allogeneic Hematopoietic Stem Cell Transplant

Experimental and Clinical Transplantation, 2021

OBJECTIVES HLA-E is located on the nonclassical major histocompatibility complex class I and acts... more OBJECTIVES HLA-E is located on the nonclassical major histocompatibility complex class I and acts as the ligand for natural killer cells. Consequently, it has a main role in the regulation of innate immune responses by involving cell identification by natural killer cells. Differences in expression levels among HLA-E alleles have been suggested to affect transplant outcomes. In this study, we evaluated the effects of different HLA-E genotypes on allogeneic hematopoietic stem cell transplant in southern Iran. MATERIALS AND METHODS We investigated 200 patients (donors and recipients) who underwent allogeneic hematopoietic stem-cell transplant and 100 normal participants (control group) in a case-control study. Detection of HLA-E polymorphisms was performed using a sequence-specific primer polymerase chain reaction method. RESULTS Statistical analyses indicated that genotypes in the transplant group were not distributed in accordance with Hardy-Weinberg equilibrium (χ²=76.56; P < .001), whereas genotypes in the control group were distributed in accordance with Hardy-Weinberg equilibrium (χ²=0.39; P = .53). No significant differences were observed in cumulative incidence of acute (P = .76; hazard ratio = 0.80; 95% confidence interval, 0.19-3.31) and chronic (P = .75, hazard ratio = 0.048; 95% confidence interval, 0.00) graft-versus-host disease in recipients harboring HLA-E∗0103 allele compared with those homozygous for the HLA-E∗0101 allele. The HLA-E∗0103 allele showed a trend toward lower cumulative incidence of relapse compared with the homozygous HLA-E∗0101 genotype (8% vs 21.5%; P = .37; hazard ratio = 2.50; 95% confidence interval, 0.32-19.20). CONCLUSIONS Genotypes of the HLA-E molecule did not correlate with acute and chronic graft-versus-host disease in hematopoietic stem cell transplant recipients except for the HLA-E∗0101∗∕∗0103 genotype, which was protective in survival of our study patients.

Optimization of activin-A: a breakthrough in differentiation of human induced pluripotent stem cell into definitive endoderm

3 Biotech, 2020

The first step in differentiation of pluripotent stem cell toward endoderm-derived cell/organ is ... more The first step in differentiation of pluripotent stem cell toward endoderm-derived cell/organ is differentiation to definitive endoderm (DE) which is the central issue in developmental biology. Based on several evidences, we hypothesized that activin-A optimization as well as replacement of fetal bovine serum (FBS) with knockout serum replacement (KSR) is important for differentiation of induced pluripotent stem cell (iPSC) line into DE. Therefore, a stepwise differentiation protocol was applied on R1-hiPSC1 cell line. At first, activin-A concentration (30, 50, 70 and 100 ng/ml) was optimized. Then, substitution of FBS with KSR was evaluated across four treatment groups. The amount of differentiation of iPSC toward DE was determined by quantitative gene expression analyses of pluripotency ( NANOG and OCT4 ), definitive endoderm ( SOX17 and FOXA2 ) and endoderm-derived organs ( PDX1 , NEUROG3, and PAX6 ). Based on gene expression analyses, the more decrease in concentrations of activin-A can increase the differentiation of iPSC into DE, therefore, 30 ng/ml activin-A was chosen as the best concentration for the differentiation of R1-hiPSC1 line toward endoderm-derived organ. Moreover, complete replacement of FBS with gradually increased KSR improved the differentiation of iPSC toward DE. For this reason, the addition of 0% KSR at day 1, 0.2% at day 2 and 2% for the next 3 days was the best optimal protocol of the differentiation of iPSC toward DE. Overall, our results demonstrate that optimization of activin-A is important for differentiation of iPSC line. Furthermore, the replacement of FBS with KSR can improve the efficiency of iPSC differentiation toward DE.

Detection of eight foodborne bacterial pathogens by oligonucleotide array hybridization

Electronic physician, 2017

Simultaneous and rapid detection of multiple foodborne bacterial pathogens is important for the p... more Simultaneous and rapid detection of multiple foodborne bacterial pathogens is important for the prevention of foodborne illnesses. The aim of this study was to evaluate the use of 16S rDNA and 23S rDNA sequences as targets for simultaneous detection of eight foodborne bacterial pathogens. Nineteen bacterial oligonucleotide probes were synthesized and applied to nylon membranes. Digoxygenin labeled 16S rDNA and 23S rDNA from bacteria were amplified by PCR using universal primers, and the amplicons were hybridized to the membrane array. Hybridization signals were visualized by NBT/BCIP color development. The eight intestinal bacterial pathogens including Salmonella enterica, Escherichia coli, Bacillus cereus, Vibrio cholerae, Shigella dysenteriae, Staphylococcus aureus, Listeria monocytogenes, and Enterococcus faecalis were appropriately detected in a panel of oligonucleotide array hybridization. The experimental results showed that the method could discriminate the bacterial pathogen...

Simultaneous Detection of Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus by Oligonucleotide Microarray

International Journal of Enteric Pathogens, 2015

Background: Traditional laboratory methods to detect pathogenic bacteria are time consuming and l... more Background: Traditional laboratory methods to detect pathogenic bacteria are time consuming and laborious. Therefore, it is essential to use powerful and reliable molecular methods for quick and simultaneous detection of microbial pathogens. Objectives: The current study aimed to evaluate the capability and efficiency of 23S rDNA sequence for rapid and simultaneous detection of four important food-borne pathogens by an oligonucleotide microarray technique. Materials and Methods: The 23S rDNA sequences of Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus were obtained from GenBank databases and used to design the oligonucleotide probes and primers by Vector NTI software. Oligonucleotide probes were placed on a nylon membrane and hybridization was performed between probes and 23S rDNA digoxigenin-labeled polymerase chain reaction (PCR) products. Hybridization signals were visualized by NBT/BCIP color development. Results: Positive hybridization color was produced for Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus. The oligonucleotide microarray detected all bacterial strains in a single reaction in less than five hours. The sensitivity of the performed microarray assay was 10 3 cfu/mL for each species of pathogen. No cross reaction was found between the tested bacterial species. Conclusions: The obtained results indicated that amplification of 23S rDNA gene followed by oligonucleotide microarray hybridization is a rapid and reliable method to identify and discriminate foodborne pathogens tested under the study.

Detection of tetracycline resistance genes from diarrheagenic E. coli by Multiplex PCR

Adaptive strategies of uropathogenic Escherichia coli CFT073: from growth in lab media to virulence during host cell adhesion

International Microbiology, 2022

Urinary tract infections (UTIs) are a major concern in public health. The prevalent uropathogenic... more Urinary tract infections (UTIs) are a major concern in public health. The prevalent uropathogenic bacterium in healthcare settings is Escherichia coli. The increasing rate of antibiotic-resistant strains demands studies to understand E. coli pathogenesis to drive the development of new therapeutic approaches. This study compared the gene expression profile of selected target genes in the prototype uropathogenic E. coli (UPEC) strain CFT073 grown in Luria Bertani (LB), artificial urine (AU), and during adhesion to host bladder cells by semi-quantitative real-time PCR (RT-PCR) assays. AU effectively supported the growth of strain CFT073 as well as other E. coli strains with different lifestyles, thereby confirming the appropriateness of this medium for in vitro models. Unexpectedly, gene expression of strain CFT073 in LB and AU was quite similar; conversely, during the adhesion assay, adhesins and porins were upregulated, while key global regulators were downregulated with respect to lab media. Interestingly, fimH and papGII genes were significantly expressed in all tested conditions. Taken together, these results provide for the first time insights of the metabolic and pathogenic profile of strain CFT073 during the essential phase of host cell adhesion.

Inflammatory Response in Caco-2 Cells Stimulated with Anisakis Messengers of Pathogenicity

by Ilaria Bellini and Meysam Sarshar

Pathogens, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more

Optimization of 3D islet-like cluster derived from human pluripotent stem cells: An efficient in vitro differentiation protocol

by Meysam Sarshar and S. Ghorbani-dalini

Gene, 2022

Development of an optimized protocol to produce sufficient functional human insulin-producing isl... more Development of an optimized protocol to produce sufficient functional human insulin-producing islet-like cluster is important as a potential therapeutic strategy for diabetes as well as in vitro studies. Here, we described a stepwise protocol for differentiation of the human induced pluripotent stem cell line (R1-hiPSC1) into the isletlike cluster using several growth factors and small molecules. Therefore, various differentiation steps have been adopted to maximize mimicking of developmental processes in order to form functional islet like cluster. The differentiation protocol enables us to generate 3D islet-like clusters with highly viable cells, which are insulin producer and glucose responsive. Transcriptome analysis of transcription factors and functional genes revealed high coordination between gene expressions and resembling to those reported during natural development of islet cell. This coordination was further confirmed by hierarchical clustering of genes during differentiation. Furthermore, the islet-like clusters were enriched with insulin producing cells and formed glucose responsiveness behavior upon stimulation with glucose. Our protocol provides a robust platform and well-behaved model for additional developmental studies and shed light our clusters as a good candidate for in vitro model. Further studies are needed to assess the hormonal content of this cluster as well as transplantation into the animal model.

The Acinetobacter baumannii model can explain the role of small non-coding RNAs as potential mediators of host-pathogen interactions

Frontiers in Molecular Biosciences, 2022

Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances i... more Bacterial small RNAs (sRNAs) research has accelerated over the past decade, boosted by advances in RNA-seq technologies and methodologies for capturing both protein–RNA and RNA–RNA interactions. The emerging picture is that these regulatory sRNAs play important roles in controlling complex physiological processes and are required to survive the antimicrobial challenge. In recent years, the RNA content of OMVs/EVs has also gained increasing attention, particularly in the context of infection. Secreted RNAs from several bacterial pathogens have been characterized but the exact mechanisms promoting pathogenicity remain elusive. In this review, we briefly discuss how secreted sRNAs interact with targets in infected cells, thus representing a novel perspective of host cell manipulation during bacterial infection. During the last decade, Acinetobacter baumannii became clinically relevant emerging pathogens responsible for nosocomial and community-acquired infections. Therefore, we also summarize recent findings of regulation by sRNAs in A. baumannii and discuss how this emerging bacterium utilizes many of these sRNAs to adapt to its niche and become successful human pathogen.

Insightful Improvement in the Design of Potent Uropathogenic E. coli FimH Antagonists

Pharmaceutics , 2023

This article is an open access article distributed under the terms and conditions of the Creative... more

The Interleukin-1 (IL-1) Superfamily Cytokines and Their Single Nucleotide Polymorphisms (SNPs)

Journal of Immunology Research

Interleukins (ILs)—which are important members of cytokines—consist of a vast group of molecules,... more Interleukins (ILs)—which are important members of cytokines—consist of a vast group of molecules, including a wide range of immune mediators that contribute to the immunological responses of many cells and tissues. ILs are immune-glycoproteins, which directly contribute to the growth, activation, adhesion, differentiation, migration, proliferation, and maturation of immune cells; and subsequently, they are involved in the pro and anti-inflammatory responses of the body, by their interaction with a wide range of receptors. Due to the importance of immune system in different organisms, the genes belonging to immune elements, such as ILs, have been studied vigorously. The results of recent investigations showed that the genes pertaining to the immune system undergo progressive evolution with a constant rate. The occurrence of any mutation or polymorphism in IL genes may result in substantial changes in their biology and function and may be associated with a wide range of diseases and d...

Biomarkers to Monitor Adherence to Gluten-Free Diet by Celiac Disease Patients: Gluten Immunogenic Peptides and Urinary miRNAs

Foods

Celiac disease (CD) is a multifactorial autoimmune enteropathy with a prevalence greater than 1% ... more Celiac disease (CD) is a multifactorial autoimmune enteropathy with a prevalence greater than 1% in the pediatric population. The only therapy for CD patients is a strict gluten-free diet (GFD). Gluten-free food contamination by other cereals during packaging and cooking or accidental ingestion of gluten may cause several intestinal and extraintestinal symptoms in CD patients. Therefore, the monitoring of gluten contamination in food and assessing the level of ingested gluten by analytical biomarkers has been of great interest in recent years. To this aim, small gluten immunogenic peptides (GIPs) obtained by the hydrolysis of gluten and present in urine and feces have been studied as biomarkers of gluten intake and to monitor adherence to GFD by CD patients. More recently, the use of circulating, fecal and urinary miRNAs has emerged as a novel diagnostic tool that can be potentially applied to assess adherence to GFD. Moreover, the presence of GIPs and miRNAs in both feces and urine...

Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach

International Journal of Molecular Sciences, 2019

Carbapenem-resistant Acinetobacter baumannii strains cause life-threatening infections due to the... more Carbapenem-resistant Acinetobacter baumannii strains cause life-threatening infections due to the lack of therapeutic options. Although the main mechanisms underlying antibiotic-resistance have been extensively studied, the general response to maintain bacterial viability under antibiotic exposure deserves to be fully investigated. Since the periplasmic space contains several proteins with crucial cellular functions, besides carbapenemases, we decided to study the periplasmic proteome of the multidrug-resistant (MDR) A. baumannii AB5075 strain, grown in the absence and presence of imipenem (IMP). Through the proteomic approach, 65 unique periplasmic proteins common in both growth conditions were identified: eight proteins involved in protein fate, response to oxidative stress, energy metabolism, antibiotic-resistance, were differentially expressed. Among them, ABUW_1746 and ABUW_2363 gene products presented the tetratricopeptide repeat motif, mediating protein-protein interactions. ...

Microbiota-Derived Extracellular Vesicles as New Systemic Regulators

Frontiers in Microbiology, 2017

Genetic diversity of clinical strains of Salmonella enterica serovar Typhimurium

Journal Mil Med, Jul 15, 2012

Aims: Salmonella spp. is one of the most common pathogenic bacteria responsible for gastroenterit... more Aims: Salmonella spp. is one of the most common pathogenic bacteria responsible for gastroenteritis in human. Among Salmonella spp., S. typhimurium has many hosts other than humans and its prevalence rate is high in society. The aim of this study was to determine the ribotype diversity of S. typhimurium stains isolated in some hospitals of Tehran, Iran. Methods: In this descriptive study, clinical samples were collected from different hospitals in Tehran were investigated. Bacterial isolation was carried out by standard procedures in selective culture media and identification was achieved through biochemical and serological methods. DNA extraction was performed by phenol-cholorophorm methods. Ribotyping was used for molecular typing of S. typhimurium clinical isolates. Results: The sizes of the ribotyping bands ranged from 1.4 to 16.8 kb in all ribotypes. The S. typhimurium isolates were divided into 7 clusters based on the diversity of ribosomal genome areas. Most isolates (5 strains) belonged to the cluster 2b. Three isolates belonged to the 6b cluster and for the rest of isolates, each belhonged to one of other clusters. Conclusion: S. typhimurium strains circulating in the studied hospitals of Tehran, do not belong to a specific ribotype and have ribotype diversity, but other molecular typing methods should be implemented in order to make a more precise judjement about the presence of whether limited or widespread clones and the relationship among the different strains of this serotype.

The Phylum Spirochaetaceae

Evaluation of OipA and DupA Genes in Helicobacter Pylori Strains and Their Relationship with Different Gastroduodenal Diseases

Abstract Background and Objectives: Helicobacter pylori cause gastroduodenal diseases. Studies su... more

Outer membrane vesicles are the powerful cell-to-cell communication vehicles that allow bacteria to monitor extracellular milieu

ExRNA

Existence of cell-to-cell communication strategies among bacteria (i.e., defined as inter-species... more Existence of cell-to-cell communication strategies among bacteria (i.e., defined as inter-species, intra-species, and inter-kingdom crosstalk) reveals how genius they are (1,2). The common and well-studied language for bacterial communication is quorum sensing (QS), an informative signaling pathway within a bacterial population (3-5). Specifically, bacteria secrete signaling modules under QS regulation, known as autoinducers (AIs), to share quorum information and regulate group behaviours. QS modulates the expression of bacterial pathogenicity factors involved in the infection process, as a similar regulation could occur in the physiology of host cells. Detailed mechanisms are extensively reviewed (6,7). Bacterial conversation enables them to feel the surrounding stimuli and coordinate their gene expression accordingly. This cooperation in sensing and responding to environmental changes could result in arrays of behaviour, ranging from symbiosis to virulence, biofilm formation, stress adaptation and natural product production, leading bacteria to live like multicellular organisms (8-10). Furthermore, bacteria need to manage competition for ecological niches and resources that favour their survival and genetic persistence. This strategy underlies mechanisms of complex interactions that occur among bacteria as well as bacteria-hosts. While the potency of QS has gained the interest of researchers for a long time, only recently QS-regulated pathways have been reported to be involved in membrane vesicles (MVs) or outer membrane vesicles (OMVs) biogenesis in Gram-positive and Gram-negative bacteria, respectively (11). OMVs have been recognized as an alternative vehicle for cell-to-cell signaling in bacteria. This spherical membranous structure can package cargoes such as virulence factors, biologically active proteins, DNA, RNA, as well as signaling molecules, playing an important role in bacterial adaptation and survival (2,12). Despite tremendous progress in the OMVs field (e.g., involvement in disease-related processes and delivery mechanisms into host cells), there is still some uncertainty in the biogenesis of OMVs and their precise sorting mechanisms within bacterial communities. So far, there is enough evidence connecting QS and OMVs, indicating that either QS molecules could serve as OMVs cargo or they are able to control the release of OMVs in several nosocomial pathogens (i.e., Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii and Escherichia coli) (13). The latter mechanism could act either by stimulating OMVs secretion, a phenomenon evidenced in P. aeruginosa, Vibrio harveyi, Stenotrophomonas maltophilia, as well as in plant pathogens such as Xanthomonas oryzae and Xanthomonas campestris or vice versa by inhibiting its release as reported in Xylella fastidiosa (14-18). For instance, through a QS-regulated process, OMVs released by the environmental pathogen Chromobacterium

Genotyping of Salmonella Enterica Serovar Enteritidis Strains Isolated from Clinical Samples by Pulsed-Field Gel Electrophoresis (PFGE)

مجله دانشکده پزشکی اصفهان, 2013

Background: The infections caused by Salmonella enterica serovar enteritidis (Salmonella enteriti... more Background: The infections caused by Salmonella enterica serovar enteritidis (Salmonella enteritidis) have been increasing in developed and developing countries. The aim of this study was to investigate the genetic relationship between the strains of Salmonella enteritidis. Methods: In a descriptive study from 2008 to 2010, clinical Salmonella enteritidis strains were collected from the patients referred to different hospitals in Tehran. The strains identified by biochemical and serological methods. Genetic relationships between the isolates were investigated using pulsed field gel electrophoresis (PFGE) method. Findings: Of 40 Salmonella enteritidis isolated strains, two PFGE profiles were obtained which among them, 32 (80%) and 8 (20%) of isolates belonged to cluster A and cluster B, respectively. Based on PFGE patterns, 28 (70%) strains exhibited nine bands and were belonged to cluster A. Conclusion: The result of this study indicated that isolated Salmonella enteritidis strains ...

The study of the oipA and dupA genes in Helicobacter pylori strains and their relationship with different gastroduodenal diseases

Aim: The purpose of this investigation was to determine the oipA and dupA genes of Helicobacter p... more Aim: The purpose of this investigation was to determine the oipA and dupA genes of Helicobacter pylori isolates from west of Iran; Chaharmahalo Bakhtiyari region and find their relationship with the severity of the gastroduodenal diseases. Background: Helicobacter pylori is an organism responsible for many gastroduodenal diseases. Many studies suggest that genetic diversity in H. pylori virulence factors such as oipA and dupA genes is high among isolates of different geographic regions and may cause more severe diseases. Patients and methods: In this cross-sectional study, gastric biopsy specimens were taken from 150 patients suffering from gastroduodenal diseases. The presence of ureC, dupA and oipA genes was tested by polymerase chain reaction (PCR). Results: Overall, 123 (82%) H. pylori strains were isolated from 150 specimens. dupA gene was detected in 41 (33.33%) H.pylori-positive specimens. There was a reverse correlation between this gene and gastric cancer. The oipA gene was...

Protective Effect of HLA-E*0101/*0103 Genotype in Survival of Patients After Allogeneic Hematopoietic Stem Cell Transplant

Experimental and Clinical Transplantation, 2021

OBJECTIVES HLA-E is located on the nonclassical major histocompatibility complex class I and acts... more OBJECTIVES HLA-E is located on the nonclassical major histocompatibility complex class I and acts as the ligand for natural killer cells. Consequently, it has a main role in the regulation of innate immune responses by involving cell identification by natural killer cells. Differences in expression levels among HLA-E alleles have been suggested to affect transplant outcomes. In this study, we evaluated the effects of different HLA-E genotypes on allogeneic hematopoietic stem cell transplant in southern Iran. MATERIALS AND METHODS We investigated 200 patients (donors and recipients) who underwent allogeneic hematopoietic stem-cell transplant and 100 normal participants (control group) in a case-control study. Detection of HLA-E polymorphisms was performed using a sequence-specific primer polymerase chain reaction method. RESULTS Statistical analyses indicated that genotypes in the transplant group were not distributed in accordance with Hardy-Weinberg equilibrium (χ²=76.56; P < .001), whereas genotypes in the control group were distributed in accordance with Hardy-Weinberg equilibrium (χ²=0.39; P = .53). No significant differences were observed in cumulative incidence of acute (P = .76; hazard ratio = 0.80; 95% confidence interval, 0.19-3.31) and chronic (P = .75, hazard ratio = 0.048; 95% confidence interval, 0.00) graft-versus-host disease in recipients harboring HLA-E∗0103 allele compared with those homozygous for the HLA-E∗0101 allele. The HLA-E∗0103 allele showed a trend toward lower cumulative incidence of relapse compared with the homozygous HLA-E∗0101 genotype (8% vs 21.5%; P = .37; hazard ratio = 2.50; 95% confidence interval, 0.32-19.20). CONCLUSIONS Genotypes of the HLA-E molecule did not correlate with acute and chronic graft-versus-host disease in hematopoietic stem cell transplant recipients except for the HLA-E∗0101∗∕∗0103 genotype, which was protective in survival of our study patients.

Optimization of activin-A: a breakthrough in differentiation of human induced pluripotent stem cell into definitive endoderm

3 Biotech, 2020

The first step in differentiation of pluripotent stem cell toward endoderm-derived cell/organ is ... more The first step in differentiation of pluripotent stem cell toward endoderm-derived cell/organ is differentiation to definitive endoderm (DE) which is the central issue in developmental biology. Based on several evidences, we hypothesized that activin-A optimization as well as replacement of fetal bovine serum (FBS) with knockout serum replacement (KSR) is important for differentiation of induced pluripotent stem cell (iPSC) line into DE. Therefore, a stepwise differentiation protocol was applied on R1-hiPSC1 cell line. At first, activin-A concentration (30, 50, 70 and 100 ng/ml) was optimized. Then, substitution of FBS with KSR was evaluated across four treatment groups. The amount of differentiation of iPSC toward DE was determined by quantitative gene expression analyses of pluripotency ( NANOG and OCT4 ), definitive endoderm ( SOX17 and FOXA2 ) and endoderm-derived organs ( PDX1 , NEUROG3, and PAX6 ). Based on gene expression analyses, the more decrease in concentrations of activin-A can increase the differentiation of iPSC into DE, therefore, 30 ng/ml activin-A was chosen as the best concentration for the differentiation of R1-hiPSC1 line toward endoderm-derived organ. Moreover, complete replacement of FBS with gradually increased KSR improved the differentiation of iPSC toward DE. For this reason, the addition of 0% KSR at day 1, 0.2% at day 2 and 2% for the next 3 days was the best optimal protocol of the differentiation of iPSC toward DE. Overall, our results demonstrate that optimization of activin-A is important for differentiation of iPSC line. Furthermore, the replacement of FBS with KSR can improve the efficiency of iPSC differentiation toward DE.

Detection of eight foodborne bacterial pathogens by oligonucleotide array hybridization

Electronic physician, 2017

Simultaneous and rapid detection of multiple foodborne bacterial pathogens is important for the p... more Simultaneous and rapid detection of multiple foodborne bacterial pathogens is important for the prevention of foodborne illnesses. The aim of this study was to evaluate the use of 16S rDNA and 23S rDNA sequences as targets for simultaneous detection of eight foodborne bacterial pathogens. Nineteen bacterial oligonucleotide probes were synthesized and applied to nylon membranes. Digoxygenin labeled 16S rDNA and 23S rDNA from bacteria were amplified by PCR using universal primers, and the amplicons were hybridized to the membrane array. Hybridization signals were visualized by NBT/BCIP color development. The eight intestinal bacterial pathogens including Salmonella enterica, Escherichia coli, Bacillus cereus, Vibrio cholerae, Shigella dysenteriae, Staphylococcus aureus, Listeria monocytogenes, and Enterococcus faecalis were appropriately detected in a panel of oligonucleotide array hybridization. The experimental results showed that the method could discriminate the bacterial pathogen...

Simultaneous Detection of Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus by Oligonucleotide Microarray

International Journal of Enteric Pathogens, 2015

Background: Traditional laboratory methods to detect pathogenic bacteria are time consuming and l... more Background: Traditional laboratory methods to detect pathogenic bacteria are time consuming and laborious. Therefore, it is essential to use powerful and reliable molecular methods for quick and simultaneous detection of microbial pathogens. Objectives: The current study aimed to evaluate the capability and efficiency of 23S rDNA sequence for rapid and simultaneous detection of four important food-borne pathogens by an oligonucleotide microarray technique. Materials and Methods: The 23S rDNA sequences of Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus were obtained from GenBank databases and used to design the oligonucleotide probes and primers by Vector NTI software. Oligonucleotide probes were placed on a nylon membrane and hybridization was performed between probes and 23S rDNA digoxigenin-labeled polymerase chain reaction (PCR) products. Hybridization signals were visualized by NBT/BCIP color development. Results: Positive hybridization color was produced for Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus. The oligonucleotide microarray detected all bacterial strains in a single reaction in less than five hours. The sensitivity of the performed microarray assay was 10 3 cfu/mL for each species of pathogen. No cross reaction was found between the tested bacterial species. Conclusions: The obtained results indicated that amplification of 23S rDNA gene followed by oligonucleotide microarray hybridization is a rapid and reliable method to identify and discriminate foodborne pathogens tested under the study.

Detection of tetracycline resistance genes from diarrheagenic E. coli by Multiplex PCR