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<jats:p>Background: Shigella spp. is the cause of dysentery and is widespread worldwide. On the other hand, antibiotic resistance is increasing in this bacterium. Bioinformatics is a new approach to vaccine and drug design involving the selection of appropriate antigens. This study aimed to design a chimeric protein consisting of IpaD, StxB, and TolC proteins from Shigella through a bioinformatics approach as an immunogen candidate.&#x0D; Methods: The sequences of ipaD, stxB, and tolC genes were obtained. Additionally, the immunogenic regions of the associated protein, physicochemical characteristics, protein structures, B and T cells epitopes, and molecular docking were determined using in silico servers. Besides, the chimeric gene was synthesized following sequence optimization by utilizing the codon usage of Escherichia coli (E. coli). The expression of the recombinant protein was confirmed via SDS-PAGE and Western blot technique.&#x0D; Results: The residues 41-160 of IpaD, 21-89 of StxB, and 40-335 of TolC were selected. According to half-life, instability, and buried indices, IpaD-StxB-TolC was selected as the best arrangement. The Ramachandran plot showed that 97.077% of the amino acids were in the favored area. Linear and conformational epitopes were also present throughout the chimeric protein sequence. Moreover, the C-ImmSim server indicated that IgG and IgM titers could reach desirable values by the third injection. Furthermore, the stability of the mRNA-optimized gene was enhanced, increasing the Codon Adaptive Index (CAI) to 0.9. Finally, the chimeric gene was transferred to E. coli BL21, and the expression of the 60.6 kDa recombinant protein was confirmed. &#x0D; Conclusion: The results indicated that the recombinant protein could act as a proper immunogen candidate against Shigella spp.&#x0D;  </jats:p>

<jats:p>Background: Evidence on seroconversion profile of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected patients is limited. We mainly aimed to evaluate seroconversion and persistence of virus-specific antibodies in patients infected by coronavirus disease 2019 (COVID-19).&#x0D; Methods: This prospective study was conducted on 118 patients with COVID-19 presentations admitted to three hospitals in Iran and recovered from the disease, during April and May 2020. Presence of COVID-19 was confirmed by Polymerase Chain Reaction (PCR) testing on nasopharyngeal swabs. Serum samples were collected at different time points, including 0-5, 6-15, 16-25, 26-35, and 36-95 days of clinical symptom onset. For measurement of SARS-CoV-2-specific IgG and IgM antibody titers, Iran's Food and Drug Administration-approved SARS-CoV-2 ELISA kits were used.&#x0D; Results: Serologic assay revealed that 37.3% of patients (n=44) were positive for IgM at 0-5 days interval after clinical symptom onset. This rate was 60.2% (n=71) for IgG. There were increasing IgM and IgG seroconversion rates during first 25 days of clinical symptom onset, but seropositivity started to decrease thereafter, which was more evident for IgM (17.9%) than IgG (58.9%) at the 36-95 days post symptoms appearance. In other words, it was found that 83.6% of IgM-positive and 32.9% of IgG-positive patients in the first month of clinical symptom onset became seronegative in the third month of clinical symptom onset.&#x0D; Conclusion: The findings demonstrated that antibody responses to SARS-CoV-2 infection were developed in recovered COVID-19 patients; however, some of them were seronegative three months after onset of relevant symptoms. Furthermore, the stability of anti-SARS-CoV-2 antibodies could also correct our expectations from COVID-19 vaccination responses.</jats:p>

<jats:p>Background: Type 2 Diabetes Mellitus (T2DM) has emerged as a major threat to global health that fosters life-threatening clinical complications, taking a huge toll on our society. More than 65 million Indians suffer from T2DM, making it one of the leading causes of death. T2DM and associated complications have to be constantly monitored and managed which reduces the overall quality of life and increases socioeconomic burden. Therefore, it is crucial to develop specific treatment and management strategies. In order to achieve this, it is essential to understand the underlying genetic causes and molecular mechanisms.&#x0D; Methods: Integrated gene network and ontology analyses facilitate prioritization of plausible candidate genes for T2DM and also aid in understanding their mechanistic pathways. In this study, T2DM-associated genes were subjected to sequential interaction network and gene set enrichment analysis. High ranking network clusters were derived and their interrelation with pathways was assessed.&#x0D; Results: About 23 significant candidate genes were prioritized from 615 T2DM-associ-ated genes which were overrepresented in pathways related to insulin resistance, type 2 diabetes, signaling cascades such as insulin receptor signaling pathway, PI3K signaling, IGFR signaling pathway, ERBB signaling pathway, MAPK signaling pathway and their regulatory mechanisms.&#x0D; Conclusion: Of these, two tyrosine kinase receptor genes-EGFR and IGF1R were identified as common nodes and can be considered to be significant candidate genes in T2DM.</jats:p>

<jats:p>Background: The present study was aimed at phyto-synthesized silver nanoparticles (AgNPs) using Amygdalus spinosissima (A. spinosissima) extract and to investigate the antibacterial, antioxidant effects, anticancer and apoptotic effects of phyto-synthe-sized AgNPs.&#x0D; Methods: The bio-fabricated AgNPs were characterized using UV-visible spectroscopy (UV-visible), X-ray Diffraction (XRD), Fourier Transform Infrared (FTIR), Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM) and Energy Disper-sive X-ray (EDX).&#x0D; Results: The phyto-synthesized AgNPs showed maximum absorption in 438 nm, in the UV-visible spectrum. XRD peaks were observed at 2θ values in 38.20°, 44.40°, 64.60°, and 77.50° which are indexed as (111), (200), (220), and (311) bands of Face-Centered Cubic (FCC) structures of silver. FTIR analysis indicated that the AgNPs were capped with A. spinosissima extract. SEM and TEM micrographs revealed that the fabricated AgNPs were spherical and the average size range was 17.89 nm. Also, the EDX results show that the content of Ag was 90%.&#x0D; Conclusion: The phyto-synthesized AgNPs had significant antibacterial activity against Gram-negative bacteria, as well as, the AgNPs exhibited great inhibitory effects on DPPH radicals and their antioxidant properties were favorably comparable to the antioxidant outcomes of ascorbic acid. Moreover, the AgNPs showed anti-cancer activity against the MCF-7 cell line with the IC50=6.1 µg/ml. Moreover, the phyto-synthesized AgNPs could induce apoptosis in the MCF-7 cell line significantly. The GC-MS analysis of the A. spinosissima extract showed that 102 bioactive phyto-chemical compounds, which be of use to the synthesis of AgNPs.    </jats:p>

<jats:p>Background: Staphylococcus epidermidis (S. epidermidis) is the most frequently isolated pathogen from prostheses infections in the body. Therefore, improving its diagnostic methods, including rapid Nucleic Acid Amplification Tests (NAAT), seems necessary. Since the first step in designing a NAAT is to find a specific sequence and all DNA targets that have been introduced so far are not completely specific, we introduced a new 100% specific DNA target sequence to identify S. epidermidis in this study.&#x0D; Methods: Modified comparative genomic analysis was used to find the best specific target sequence to detect S. epidermidis. A PCR method was designed for the evaluation of this target. To determine the detection limit and analytical specificity, pure genomic DNA of 18 bacteria include 12 standard strains (one S. epidermidis and 11 non-S. epidermidis) and six clinical isolates (five S. epidermidis and one non-S. epidermidis) were used.&#x0D; Results: The 400 bp sequence of S. epidermidis ATCC 14990 was identified as the most specific sequence (Se400), having a 100% sequence similarity to S. epidermidis genomes but not with other bacteria. The detection limit of Se400-PCR was 10 fg, equal to about 4 copies of S. epidermidis genomic DNA/μl. All pure DNA templates from S. epidermidis generated a detectable amplicon by 264 bp length, but the PCR test was negative for the non-S. epidermidis group.&#x0D; Conclusion: The Se400 sequence can be considered as a specific target for detecting S. epidermidis, based on our findings.</jats:p>

<jats:p>Background: Rheumatoid Arthritis (RA) has multifactorial etiology and numerous genetic and environmental factors have been related to an increased risk of RA. Recently, Genome-Wide Association Studies (GWAS) suggested a large number of Single Nucleotide Polymorphisms (SNPs) loci affecting the susceptibility to RA. One of these loci is rs6859219 (C&gt;A), a functional polymorphism in the ANKRD55 gene which was associated with the expression of ANKRD55 and IL6ST. In the current study, we evaluated the possible association between rs6859219 (intronic variant) in the ANKRD55 gene with RA risk in the Iranian population.&#x0D; Methods: A case-control study using 118 RA patients and 115 healthy counterparts was undertaken in order to determine rs6859219 genotypes using real‑time polymerase chain reaction High‑Resolution Melting (HRM) method.&#x0D; Results: There was a significant difference in the genotype and allele frequencies of rs6859219 between patients and controls (p&lt;0.001). Logistic regression analysis demonstrates that CC genotype and C allele increased the risk of RA (OR for CC genotype= 7.12; 95%CI [3.51-15.05]/ OR for C allele=4.16; 95%CI [2.78-6.28]). Furthermore, regarding the dominant and recessive model of inheritance, RA patients indicated obvious association of the rs6859219 variant compared to healthy controls (p&lt;0.001). Moreover, in the patient group, there was a significant correlation between C-Reactive Protein (CRP) concentration with rs6859219 polymorphism (p&lt;0.001).&#x0D; Conclusion: Our findings propose a substantial correlation between rs6859219 polymorphism and RA risk and clinical characteristics of this disease in the Iranian population.</jats:p>

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<jats:p>Background: Toll-Like Receptors (TLRs) are the critical mediators of inflammatory routs in the gut, which play an essential role in regulating the immune responses towards various ligands derived from pathogenic bacteria. Also, TLR signaling has been implicated in the development of Inflammatory Bowel Disease (IBD), Adenomatous Polyp (AP), and Colorectal Cancer (CRC). Here, we aimed to examine the expression of some TLRs concerning certain fecal bacteria in AP and CRC patients with and without IBD.&#x0D; Methods: This case-control study collected fecal and colonic tissue samples from 93 patients versus Normal Controls (NC) via colonoscopy. Fecal samples were used for DNA extraction, and the abundance of selected fecal bacteria was determined by absolute real-time PCR. Also, the gene expression of TLR2, 4, and 5 was analyzed using RT-PCR on the colonic tissues of participants.&#x0D; Results: Compared to NC individuals, in AP and CRC patients, the mRNA expressions of TLR4 and TLR2 were significantly increased while TLR5 was decreased. A meaningful association between TLRs mRNA expression levels and the abundance of some selected fecal bacteria was detected. Also, there was a significant relationship between participant’s food regimes, smoking habit and intestinal TLRs expression.&#x0D; Conclusion: Our study proposed the important role of TLRs during adenomatous and CRC formation. Alterations in TLRs expression associated with certain gut bacteria may contribute to disease development.</jats:p>

<jats:p>Background: Bacteriophages are bacterial parasites. Unlike lytic bacteriophages, lysogenic bacteriophages do not multiply immediately after entering the host cells and may integrate their genomes into the bacterial genomes as prophages. Prophages can include various phenotypic and genotypic effects on the host bacteria. Enterococcus spp. are Gram-positive bacteria that cause infections in humans and animals. In recent decades, these bacteria have become resistant to various antimicrobials, including vancomycin. The aim of this study was to analyze genome of an enterococcal prophage.&#x0D; Methods: In this study, Enterococcus faecium EntfacYE was isolated from biological samples and its genome was analyzed using next-generation sequencing method.&#x0D; Results: Overall, 254 prophage genes were identified in the bacterial genome. The prophage included 39 housekeeping, 41 replication and regulation, 80 structural and packaging, and 48 lysis genes. Moreover, 46 genes with unknown functions were identified. All genes were annotated in DNA Data Bank of Japan.&#x0D; Conclusion: In general, most prophage genes were linked to packaging and structure (31.5%) gene group. However, genes with unknown functions included a high proportion (18.11%), which indicated necessity of further analyses. Genomic analysis of the prophages can be effective in better understanding of their roles in development of bacterial resistance to antibiotics. Moreover, identification and study of prophages can help researchers develop genetic engineering tools and novel infection therapies.</jats:p>

<jats:p>Background: Antibiotic resistance is an important concern for the public health authorities at global level. It is detrimental to human and environmental ecosystems, thus, there is a big need for natural bioactive compounds. In this work, we aimed to find out biomolecules derived from marine bacteria that may constitute an alternative to antibiotics.&#x0D; Methods: We isolated and identified thirty one marine bacteria collected from deep ocean water in central coast of Safi city, Morocco. Then, we induced biomolecules production in six marine bacterial strains. The extracts were tested for their antibacterial activity against gram-negative and gram-positive bacteria such as Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 33592 and Listeria monocytogenes ATCC 19117. Furthermore, we partially analyzed the chemical composition of these biomolecules and evaluated their sensibility to different temperatures.&#x0D; Results: The six marine bacteria were able to produce molecules which inhibited the three pathogenic strains with high inhibition zones reaching 27 mm. These molecules were characterized by heat stability from 60 to 121°C relying on each strain.&#x0D; Conclusion: The produced molecules may offer a great potential to pharmaceutical industries as they may constitute an alternative to antibiotics that are becoming less effective due to the emergence of drugs resistance.</jats:p>