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Introduction: Collagens are the most abundant proteins in the human body, accounting for one-third of total proteins. Over the last few years, accumulated evidence have indicated that some collagens are differentially expressed in cancer. The aim of the study was to assess COL1A1 gene expression as a novel marker for the progression of hepatitis B cirrhosis into hepatocellular carcinoma. Methods: This cohort study included 348 subjects and was conducted between May 2018 and June 2019. Subjects were divided into 4 groups: group1 included HBV positive hepatocellular carcinoma patients “HCC” (n= 87), group II included HBV positive patients with liver cirrhosis “LC” (n = 87), group III included chronic hepatitis B patients with neither HCC nor cirrhosis “ C-HBV” (n = 87) and group IV consisted of healthy volunteers as controls (n = 87). Fasting venous blood samples (10 ml) were collected from each participant in this study and were used for assessment of aspartate aminotransferase (AST), alanine aminotransferase (ALT), total bilirubin, albumin and alfa-fetoprotein (AFP). Another portion of blood was collected in 2 vacutainer tubes containing EDTA, one for Complete blood count and the other for gene expression of COL1A1. Results: The gene expression of collagen was 6.9 ± 8.8 in group 1 (HBV positive hepatocellular carcinoma patients) and this was a significant increase in comparison with the other groups. In group 2 (HBV positive patients with liver cirrhosis), the gene expression (collagen) was 3.7±1.5 and it was significantly increased when compared with group 4 (healthy volunteers). Conclusion: COL1A1 gene expression can be used as an indicator of the progression of hepatitis B cirrhosis into hepatocellular carcinoma.

Background: Polymorphisms of genes encoding the pro-inflammatory and anti-inflammatory cytokines can affect the clinical presentation of the infection. We aimed to assess the role of EGF gene single-nucleotide polymorphism in the outcome of chronic hepatitis B virus (HBV) infection in children. Methods: One hundred HBV-infected children and 75 healthy matched controls were enrolled in this prospective study. Patients included 18 chronic inactive and 82 chronic active carriers. EGF rs4444903 A>G genotypes were determined using allele-specific amplification. Results: Significant differences regarding EGF genotypic frequency (p=0.001) in patients compared to controls (p=0.001). Eighteen percent were inactive, and 82% were active carriers. AA, AG and GG genotypic frequency were 66.7%, 33.3%, 0% and were 3.7%, 37.8% and 58.5% in the inactive and active carriers, respectively, with significant differences regarding AA, AG, GG genotypic frequency (p=0.001 for all). EGF AA, AG, GG genotypes frequency were 1.9%, 33.3%, and 64.8%, respectively, with significant differences between cirrhotic and non-cirrhotic patients regarding AA, AG, GG genotypic frequency (p=0.001 for all). Conclusion: Increased G allele frequency in EGF rs4444903 A > G polymorphism in HBV- Egyptian children is associated with worse outcomes.

Aim: Inhibition of some quorum sensing (QS) regulated virulence factors via using non-antibiotic helping drugs to overcome antibiotic resistance problem. Introduction: P. aeruginosa is one of the major causes of fatal health care-associated infection. P. aeruginosa’s virulence factors are highly controlled by QS systems which lead to antibiotics resistance. Targeting QS may be a promising therapeutic hope for P. aeruginosa infections. Methods: Molecular Docking was performed by Shroedinger 2016 using the required constraints in the binding sites of the Las & Rhl receptor proteins of P. aeruginosa to estimate the expected activity of (quercetin and meloxicam) and compare them with great docking scores compounds like rosmarinic acid. PAO1 was used as reference strain with other P. aeruginosa strains (clinical samples). An antibiotic sensitivity test was performed to evaluate antibiotic resistance. The minimum inhibitory concentration (MIC) of tested drugs were also measured against the resistant strains. Virulence factors thanked for QS (protease, pyocyanine, rhamnolipids) and biofilm formation of selected strains were assessed before and after treatment with quercetin & meloxicam. Results and conclusion: In silico studies indicated that quercetin and meloxicam could act as inhibitors for the auto-inducer molecules as they have a high affinity for the regulatory proteins of the QS system lasR and rhlR. The experimental study of quercetin and meloxicam against P. aeruginosa showed that at sub-MIC, both drugs reduced biofilm formation and some tested virulence factors. Treatment of P. aeruginosa infection using QS inhibitors is expected and this approach may overcome the antibiotic resistance problem.

Carbapenem resistant Acinetobacter baumannii (CRAB) have become a serious problem in health care settings. Its high prevalence has been associated with nosocomial transmission, high mortality rates, drug resistance and massive economic loss. The most frequent mechanisms of resistance are carbapenem-hydrolyzing class D β-lactamases (CHDL), followed by class B metallo-β-lactamases (MBL). New Delhi metallo-β-lactamase-1(NDM-1) generated much global alarm and were labeled as superbugs which documented impossible to be treated. Preceding our study, eight different antibiotic combinations were evaluated using checkerboard method. This was based on the results obtained from antimicrobial susceptibility testing and phenotypic detection of metallo-β-lactamase production of 27 CRAB selected from our previous work. The existence of NDM-1 gene was tested using two different methods. All antibiotic combinations showed synergistic significant results and no antagonism activity was found. The percentage of NDM-1 gene in the first detection procedure was 12/27 (44.44%) were positive while the other negative 15 ones, 10/15 (66.67%) poses NDM-1were found when using the second method. PCR products were then verified by DNA sequencing. The final consensus sequences were analyzed and submitted to NCBI GenBank data base, representing accession numbers: (HQ6526091), (MK682763.1), (MK682764.1), (MK682767.1), (MN251665.1), (MN251666.1) and (MN251670.1). The alignments showed similarity ranged from 94%-100% nucleotides identity. We concluded that detection of CRAB using accurate, rapid methods and supplying hospital laboratories with molecular department for typing of pathogenic bacteria are essential. Each hospital should establish its own policies according to their antibiogram, national and international guidelines. Primary caretakers should comply with the implemented policies.

Background & Aims: Several studies, in different populations, have focused on the role of HLA-DQ gene polymorphism in the pathogenesis of HBV infection. However, these findings are still controversial. This study aimed to determine HLA-DQ polymorphism in Chronic HBV patients and its impact on the response to antiviral therapy. Methods: This study was carried out on a total number of 188 participants, they were subdivided as follows: Group I (patients’ group): included 97 patients with chronic hepatitis B viral infection that was further subdivided according to response to treatment into responder and non-responder subgroups, Group II (Control group): included 91 normal healthy subjects who were matched to the patient group by sex and age. PCR (Polymerase Chain Reaction) testing, for HBV-DNA, was done for all participants enrolled in the study to measure the viral virus load before and after treatment. HLA- DQ polymorphism allelic discrimination assay was assayed using the Real-time equipment. Results: In a general analysis for the SNP rs7453920, the overall genotypes frequencies were 37% for A/A, 60.6% for A/G, and 37% for G/G. The G alleles of HLA-DQ rs7453920 were significantly increased in chronic HBV infection patients. A total of 77 (79.4%) patients were responders. Among this group, 72.7% were male, and the average age was 38.59 ±9.15 years. On evaluation of the association between polymorphisms in HLA-DQ gene and treatment response, the results indicated that response to treatment declined when patients were carrying the more unfavorable rs 7453920 GG with a response rate of 64%. Patients carrying the mutant allele AG, or the wild type allele AA were more likely to achieve a higher rate of response (84.8% and 83.3%, respectively). Conclusion: The presence of HLA-DQB2 rs 7453920-G serves as a risk factor for chronic HBV infection and treatment failure in the Egyptian population.

Nipah virus is one of the most harmful emerging viruses with deadly effects on both humans and animals. Because of the severe outbreaks, in 2018, the World Health Organization focused on the urgent need for the development of effective solutions against the virus. However, up to date, there is no effective vaccine against the Nipah virus in the market. In the current study, the complete proteome of the Nipah virus (nine proteins) was analyzed for the antigenicity score and the virulence role of each protein, where we came up with fusion glycoprotein (F), glycoprotein (G), protein (V), and protein (W) as the candidates for epitope prediction. Following that, the multitope vaccine was designed based on top-ranking CTL, HTL, and BCL epitopes from the selected proteins. We used suitable linkers, adjuvant, and PADRE peptides to finalize the constructed vaccine, which was analyzed for its physicochemical features, antigenicity, toxicity, allergenicity, and solubility. The designed vaccine passed these assessments through computational analysis and, as a final step, we ran a docking analysis between the designed vaccine and TLR-3 and validated the docked complex through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for Nipah virus. Here, we describe the computational approach for design and analysis of this vaccine.

Malassezia furfur is the main causative species in pityriasis versicolor infections and is now widely believed to be a part of the skin microbiota, yet it was systematically missed in the early skin metagenomic studies. Here, we curated a specific set of M. furfur sequences and used them to reanalyze publicly available skin metagenomes to computationally investigate the distribution of M. furfur and its relative abundance at different skin sites. To this end, we used BLASTN to match and align these marker genes to the selected metagenomic datasets and estimated M. furfur relative abundance as the number of BLASTN hits per million metagenomic reads. We found a relative enrichment of M. furfur in the retro auricular crease, the antecubital fossa, and the forehead. Among skin categories, sebaceous areas were the most significantly enriched in M. furfur, while in terms of exposure/occlusion, exposed areas had the highest abundance. This work will facilitate and allow the estimation and correction of past estimates of this important fungal species in shot gun metagenomic data sets.

During the current era of the COVID-19 pandemic, the dissemination of Mucorales has been reported globally, with elevated rates of infection in India, and because of the high rate of mortality and morbidity, designing an effective vaccine against mucormycosis is a major health priority, especially for immunocompromised patients. In the current study, we studied shared Mucorales proteins, which have been reported as virulence factors, and after analysis of several virulent proteins for their antigenicity and subcellular localization, we selected spore coat (CotH) and serine protease (SP) proteins as the targets of epitope mapping. The current study proposes a vaccine constructed based on top-ranking cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes from filtered proteins. In addition to the selected epitopes, β-defensins adjuvant and PADRE peptide were included in the constructed vaccine to improve the stimulated immune response. Computational tools were used to estimate the physicochemical and immunological features of the proposed vaccine and validate its binding with TLR-2, where the output data of these assessments potentiate the probability of the constructed vaccine to stimulate a specific immune response against mucormycosis. Here, we demonstrate the approach of potential vaccine construction and assessment through computational tools, and to the best of our knowledge, this is the first study of a proposed vaccine against mucormycosis based on the immunoinformatics approach.

Unfortunately, the affiliation of author "Rania Abdelmonem Khattab" was published incorrectly in the original publication. The correct version of affiliation is updated here.