Gut-Lung Microbiota Characterization in Patients with Non-Small Cell Lung Carcinoma and COVID-19 Coinfection.

BACKGROUND: Non-small cell lung cancer (NSCLC) patients with COVID-19 have an excessive chance of morbidity and mortality. The fecal-nasopharyngeal microbiota compositions of NSCLC patients were assessed in this study. METHODS: In total, 234 samples were collected from 17 NSCLC patients infected with COVID-19, 20 NSCLC patients without confirmed COVID-19, 40 non NSCLC patients with COVID-19, and 40 healthy individuals. RESULTS: In lung microbiota, the abundance of Streptococcus spp. in NSCLC patients with confirmed COVID-19 was significantly higher than the two control groups. Pseudomonas aeruginosa and Staphylococcus aureus were listed as the most frequent pulmonary bacterial groups that colonized COVID-19 patients. In fecal specimens, the numbers of Bacteroidetes, Firmicutes, and Actinobacteria phyla were significantly higher amongst NSCLC patients with COVID-19. NSCLC patients infected with COVID-19 showed lower levels of Lactobacillus spp., Akkermansia muciniphila, and Bifidobacterium spp. The counts of Streptococcus spp., in NSCLC patients with COVID-19 were significantly higher than those of healthy individuals (8.49±0.70 log CFU/g wet feces vs 8.49±0.70 log CFU/g wet feces). Prevotella spp. were enriched in the gut and respiratory tracts of COVID-19 patient groups. The unbiased analysis showed an increment in Enterococcus spp., Streptococcus spp., and Prevotella spp. CONCLUSION: Eventually, it was found that compared to control groups, COVID-19 patients with NSCLC showed diminished gut bacteria diversity and increase in Lactobacillus spp., A. muciniphila, and Bifidobacterium spp. The overgrowth of Enterococcus spp., Streptococcus spp., and Prevotella spp. could be potential predictive biomarkers in the gut-lung axis of NSCLC patients with COVID-19.

Different aspects in explaining how mutations could affect the binding mechanism of receptor binding domain of SARS-CoV-2 spike protein in interaction with ACE2.

During replication, some mutations occur in SARS-CoV-2, the causal agent of COVID-19, leading to the emergence of different variants of the virus. The mutations that accrue in different variants of the virus, influence the virus' ability to bind to human cell receptors and ability to evade the human immune system, the rate of viral transmission, and effectiveness of vaccines. Some of these mutations occur in the receptor binding domain (RBD) of the spike protein that may change the affinity of the virus for the ACE2 receptor. In this study, several in silico techniques, such as MD and SMD simulations, were used to perform comparative studies to deeply understand the effect of mutation on structural and functional details of the interaction of the spike glycoprotein of SARS-CoV-2, with the ACE2 receptor. According to our results, the mutation in the RBD associated with the Omicron variant increase binding affinity of the virus to ACE2 when compared to wild type and Delta variants. We also observed that the flexibility of the spike protein of the Omicron variant was lower than in comparison to other variants. In summary, different mutations in variants of the virus can have an effect on the binding mechanism of the receptor binding domain of the virus with ACE2.

A Process Evaluation of the Isfahan Antibiotic Awareness Campaign: Developing Engagement on Antimicrobial Resistance.

Background: One of the most prominent global health threats is antibiotic resistance, leading to infection treatment failure. The first Iranian antibiotic awareness week campaign was initiated to improve the prudent use and wise prescription of antibiotics. Materials and Methods: The Isfahan antibiotic awareness campaign was held from November 30 to December 6, 2019, among two targeted populations; the general population and health-care workers by Isfahan University of Medical Sciences. In this campaign held in the main squares, streets, and a city's referral hospital, various educational methods were used to aware and sensitize the general population and medical staff about antibiotics and microbial resistance. These methods include face-to-face training, brochures, advertisement posters and billboards around the city, educational videos, social media messages, retraining for medical doctors and medical specialists, and interviewing in the Islamic Republic of Iran Broadcast. Results: Two hundred and twenty general practitioners, medical specialists, and residents participated in two retraining educational conferences in Al-Zahra Hospital, Isfahan, Iran. The mean score satisfaction of the two conferences was three from four. Nearly 2000 of the general population were under face-to-face educational programs whom after that, 83.6% had the correct answer to the questions around antimicrobial awareness. Conclusions: This campaign was an excellent experience as a pilot study with appealing issues. Further, activities are required to improve engagement with the target population and determine the impact of this campaign on antibiotic consumption and prescription behavior among the public and health-care professionals.

Dysregulation of RNA interference components in COVID-19 patients.

OBJECTIVE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the novel coronavirus causing severe respiratory illness (COVID-19). This virus was initially identified in Wuhan city, a populated area of the Hubei province in China, and still remains one of the major global health challenges. RNA interference (RNAi) is a mechanism of post-transcriptional gene silencing that plays a crucial role in innate viral defense mechanisms by inhibiting the virus replication as well as expression of various viral proteins. Dicer, Drosha, Ago2, and DGCR8 are essential components of the RNAi system, which is supposed to be dysregulated in COVID-19 patients. This study aimed to assess the expression level of the mentioned mRNAs in COVID-19patients compared to healthy individuals. RESULTS: Our findings demonstrated that the expression of Dicer, Drosha, and Ago2 was statistically altered in COVID-19 patients compared to healthy subjects. Ultimately, the RNA interference mechanism as a crucial antiviral defense system was suggested to be dysregulated in COVID-19 patients.

The Relationship Between HCV-NS5A Gene Mutations and Resistance to Combination Therapy in Patients with HCV- Genotype 1-B.

BACKGROUND: Hepatitis C virus (HCV) is one of the major causes of chronic liver disease, as it holds a significant role in developing liver cirrhosis and hepatocellular carcinoma. Combination therapy with Pegaferon and Ribavirin leads to viral clearance of only 50% of patients. During the host antiviral response, protein kinase R (PKR) interacts with eukaryotic translation initiation factor 2 alpha (eIF2α), that leads to the inhibition of viral protein synthesis. The viral NS5A protein appears to interfere with this antiviral action, evading the host immune response. However, mutations in the NS5A gene have been observed to render HCV more susceptible to treatment. The aim of this study was to determine the mutations present in the IFN Sensitivity Determining Region (ISDR) and NS5A-PKRbinding domain regions in chronic HCV infected patients before and after therapy. METHODS: Viral RNA was isolated from the plasma of 52 chronic HCV infected patients before and after treatment. RT-Nested PCR reaction was used to reverse transcription and amplification of target fragment using the specific primers. RESULTS: Sequence analysis revealed no relationship between NS5A mutations and response to treatment. No significant difference was found between the mutations before and 3 months after treatment among responders and non-responders. CONCLUSION: This study showed that the number of mutations in NS5A did not significantly differ between the patients who responded to treatment and the patients that did not. Therefore, sequencing of these regions does not appear to be a suitable tool for predicting treatment outcomes.

Vaccine design and delivery approaches for COVID-19.

COVID-19 is still a deadly disease that remains yet a major challenge for humans. In recent times, many large pharmaceutical and non-pharmaceutical companies have invested a lot of time and cost in fighting this disease. In this regard, today's scientific knowledge shows that designing and producing an effective vaccine is the best possible way to diminish the disease burden and dissemination or even eradicate the disease. Due to the urgent need, many vaccines are now available earlier than scheduled. New technologies have also helped to produce much more effective vaccines, although the potential side effects must be taken into account. Thus, in this review, the types of vaccines and vaccine designs made against COVID-19, the vaccination programs, as well as the delivery methods and molecules that have been used to deliver some vaccines that need a carrier will be described.

Novel and emerging mutations of SARS-CoV-2: Biomedical implications.

Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 virus strains has geographical diversity associated with diverse severity, mortality rate, and response to treatment that were characterized using phylogenetic network analysis of SARS-CoV-2 genomes. Although, there is no explicit and integrative explanation for these variations, the genetic arrangement, and stability of SARS-CoV-2 are basic contributing factors to its virulence and pathogenesis. Hence, understanding these features can be used to predict the future transmission dynamics of SARS-CoV-2 infection, drug development, and vaccine. In this review, we discuss the most recent findings on the mutations in the SARS-CoV-2, which provide valuable information on the genetic diversity of SARS-CoV-2, especially for DNA-based diagnosis, antivirals, and vaccine development for COVID-19.

The effect of public health educational campaign regarding antibiotic use and microbial resistance on knowledge, attitude, and practice in the Iran.

INTRODUCTION: The aim of the present study was to show the effect of public health educational campaign regarding antibiotic use and microbial resistance on knowledge, attitude, and practice of people in Isfahan. MATERIALS AND METHODS: This quasi-experimental study was conducted in October 2019 on the public population in Isfahan (a city in the center of Iran). Simple random sampling was done in ten urban areas.). A total of 708 people participated in the study. For assessing the knowledge, attitude, and practice a related researchers-made questionnaire was used in the present study. Finally, data were entered into SPSS (20) and analytical statistics including paired t-test were used. The statistical significance level was considered <0.05. RESULTS: The majority of participants in this study were female 434 (61.9%) and the rest of them were male. The mean ± standard deviation of age was 31.68 (11.11), range of 11-67. More than 50 present of participants had a Bachelor's degree (37.7%) and diploma (27.7%). Most individuals were self-employed 277 (43.1%). About the type of marriage, 54.89% were single and others were married. Results showed that the mean of knowledge and attitude was increased after the intervention (P < 0.05). CONCLUSION: Increase knowledge between people, adherence to treatment and minimizes healthcare costs, however, "antibiotics are misused so often because of the belief that these are benign drugs. In the absence of urgent corrective and protective actions, the world is heading towards a postantibiotic era, in which many common infections will no longer have a cure and once again, kill unabated.

Recent developments in antibody derivatives against colorectal cancer; A review.

Colorectal cancer (CRC) is the fourth most common cause of cancer and mortality worldwide and is the third most common cancer in men and women. Surgery, radiotherapy, and chemotherapy are conventionally used for the treatment of colorectal cancer. However, these methods are associated with various side effects on normal cells. Thus, new studies are moving towards more effective and non-invasive methods for treatment of colorectal cancer. Targeted therapy of CRC is a promising new approach to enhance the efficiency and decrease the toxicity of the treatment. In targeted therapy of CRC, antibody fragments can directly inhibit tumor cell growth and proliferation. They also can act as an ideal carrier for targeted delivery of anticancer drugs. In the present study, the structure and function of different formats of antibody fragments, immune-targeted therapy of CRC using antibody fragments will be discussed.

Antimicrobial Activities of Satureja khuzestanica Jamzad; A Review.

Satureja khuzestanica Jamzad is a species native to Iran and is highly important in Southwestern regions. It belongs to the Lamiaceae family and grows in different climates. A number of pharmacological properties such as analgesic, anti-inflammatory, anticancer, anti-thyroid, antioxidant, and diuretic have been attributed to this plant. In recent years, a wide range of biological properties, extract, and essential oil of Satureja khuzestanica has been studied by researchers. In the present study, Scopus, SID, ISI, Google Scholar, and PubMed indices were used to extract research articles. No publication time constraint was considered, and the keyword "Satureja khuzestanica" was used to search articles. All extracted articles were examined by two expert researchers and those on the biologic and fundamental science properties of this plan entered the study. Results showed that S. khuzestanica has extensive research and medicinal applications. Considering the economic and medical importance of S. khuzestanica, it is hoped that more extensive studies can be conducted in the future on the use of compounds and derivatives of this plant in order to obtain herbal medications to treat pathogens in human and animal.

Bio-inspired silver selenide nano-chalcogens using aqueous extract of Melilotus officinalis with biological activities.

For the first time, an aqueous extract of Melilotus officinalis was used to synthesize bimetallic silver selenide chalcogenide nanostructures (Ag2Se-NCs). The formation of NCs was confirmed and characterized by UV-visible and FTIR spectroscopy, SEM and TEM imaging, XRD and EDX crystallography, zeta potential (ZP) and size distribution (DLS). The bioactivities of biosynthesized Ag2Se-NCs, such as antibacterial, antibiofilm, antioxidant and cytotoxicity potentials, were then examined. Bio-based Ag2Se-NCs were successfully synthesized with mostly spherical shape in the size range of 20-40 nm. Additionally, the MIC and MBC values of Ag2Se-NCs against ß-lactam-resistant Pseudomonas aeruginosa (ATCC 27853) were 3.12 and 50 µg/ml, respectively. The DPPH scavenging potential of Ag2Se-NCs in terms of IC50 was estimated to be 58.52. Green-synthesized Ag2Se-NCs have been shown to have promising benefits and could be used for biomedical applications. Although the findings indicate promising bioactivity of Ag2Se-NCs synthesized by M. officinalis extract (MO), more studies are required to clarify the comprehensive mechanistic biological activities.

An update on antiviral antibody-based biopharmaceuticals.

Due to the vastness of the science virology, it is no longer an offshoot solely of the microbiology. Viruses have become as the causative agents of major epidemics throughout history. Many therapeutic strategies have been used for these microorganisms, and in this way the recognizing of potential targets of viruses is of particular importance for success. For decades, antibodies and antibody fragments have occupied a significant body of the treatment approaches against infectious diseases. Because of their high affinity, they can be designed and engineered against a variety of purposes, mainly since antibody fragments such as scFv, nanobody, diabody, and bispecific antibody have emerged owing to their small size and interesting properties. In this review, we have discussed the antibody discovery and molecular and biological design of antibody fragments as inspiring therapeutic and diagnostic agents against viral targets.

Emerging Involvement of long non-coding RNAs in gastrointestinal associated inflammatory disorders.

Gastrointestinal (GI) disorders including a wide range of infectious, inflammatory, autoimmune, etc. disorders. Inflammatory bowel and celiac disease are non-fatal but overwhelming GI associated disorders. IBD and celiac's complications, besides the great suffering, disturb the normal life of the patients and make them involved in mental and physical problems. The emerging role of genetic content is deniable for GI inflammatory disorders incidence, and long non-coding RNAs (lncRNAs) function is the recent topic for its association. Analyzing of absolute lncRNAs interference in GI inflammatory appearance remains in infancy, and more studies are requested. Here, we concisely performed a systematic review in the last knowledge up to 2020 to identify all of the significant lncRNAs associated with the initiation and progression of GI inflammatory diseases. Accordingly, this assay attempted to refer to the expression of lncRNAs changing from the normal state, discovery of genetic mechanisms, and main effectors that would trigger associated IBD and celiac expression and immune responses would be effective for therapeutic approaches. It could be useful for prognostic and diagnostic purposes of GI associated inflammatory disorders.

Evaluation of antimicrobial activity of synthesised silver nanoparticles using Thymus kotschyanus aqueous extract.

Development of a green chemistry process for the synthesis of silver nanoparticles (AgNPs) has become a focus of interest. Characteristics of AgNPs were determined using techniques, such as ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FTIR) analysis, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy and X-ray diffraction (XRD). The synthesised AgNPs using Thymus kotschyanus had the most growth inhibition against gram-positive bacteria such as Staphylococcus aureus and Bacillus subtilise, while the growth inhibition of AgNPs at 1000-500 µg/ml occurred against Klebsiella pneumonia and at 1000-250 µg/ml of AgNPs was observed against E. coli. The UV-vis absorption spectra confirmed the formation of the AgNPs with the characteristic peak at 415 nm and SEM micrograph acknowledged spherical particles in a nanosize range. FTIR measured the possible biomolecules that are responsible for stabilisation of AgNPs. XRD analysis exhibited the crystalline nature of AgNPs and showed face-centred cubic structure. The synthesised AgNPs revealed significant antibacterial activity against gram-positive bacteria.

Cytotoxic Effects of Coated Gold Nanoparticles on PC12 Cancer Cell.

BACKGROUND: The use of gold nanoparticles in medicine and especially in cancer treatment has been of interest to researchers. The effectiveness of this nanoparticle on cells significantly depends on the amount of its entry into the cells. This study was performed to compare the rate and mechanism of effect of gold nanoparticles coated with different amino acid on PC12 cancer cell line. MATERIALS AND METHODS: The PC12 cells line were exposed to various concentrations of amino acid coated and uncoated gold nanoparticles (0.5, 2.5 and 5 µM). Cell death rate was determined according to level of Lactate dehydrogenase (LDH) release from cells and MTT assay. In addition cell morphology and the amount of Cellular Reactive oxygen species (ROS) were studied. RESULTS: The uncoated gold nanoparticles have shown minor effects on cellular life. Gold nanoparticles coated by tryptophan at high concentrations (2.5, 5 and 25µM) increase in cancer cells metabolic activity. Gold nanoparticles coated by Aspartate also produce the largest amount of LDH and ROS in cancer cells and therefore caused of highest rate of apoptosis. CONCLUSION: The results showed that the nanoparticles coated with amino acids are affected on cellular metabolism and apoptosis more than uncoated nanoparticles. Also the smallest coated nanoparticles (coated by aspartate) have the most influence and by increasing the size, this effect was reduced.

The relationship between HLA-G and viral loads in non-responder HCV-infected patients after combined therapy with IFN-α2α and ribavirin.

Hepatitis C disease is a virus mediated infection causing major health problem worldwide. Conversions of immune surveillance play an important role in response to virus clearance. Immune modulating molecules such as HLA-G and IL-10 that convert immune response toward Th2 may play a role to inhibit response from combined therapy with IFN-α2α and ribavirin. The objective of this study was to investigate the expression of HLA-G and IL-10 in responder and non-responder HCV positive patients. In this study, characteristics of the virus and 48 responder and non-responder patients in response to the combined therapy with IFN-α2α and ribavirin were analyzed. The expression levels of HLA-G and IL-10 were conducted using real-time PCR. Also, soluble HLA-G in both groups of patients and healthy individuals were determined by enzyme-linked immunosorbent assay. According to the obtained data, HCV 1a was the predominant genotype in responder and non-responder patients. Expression levels of HLA-G and IL-10 in non-responder group was significantly more than responder and control groups (P<0.001). Additionally, expression levels of HLA-G and IL-10 were remarkably higher compared to healthy individuals at the beginning of treatment. Soluble HLA-G in non-responder patients was noticeably increased in comparison to responder patients after treatment (P<0.05). These findings suggest that elevation of HLA-G and IL-10 in HCV infected patients may play an important role in response to combined therapy with IFN-α2α and ribavirin.

Association of SNPs in interferon receptor genes in chronic hepatitis C with response to combined therapy of interferon and ribavirin.

Hepatitis C Virus is one of the main reasons for chronic liver disease and hepatocellular carcinoma. Combination therapy with Interferon (peg-IFN-α) and Ribavirin (RBV) clear the virus more likely than the others. Different factors like virus and host characteristics influence on response to treatment. The most important viral factors include virus genotype and viral load; host factors like genetic, gender, race, age, weight and liver enzymes are also important. Previous studies have shown that single nucleotide polymorphisms (SNPs) in IFNR genes can regulate and influence on treatment with IFN. The purpose of this study is to investigate the association between SNPs in IFN-α receptor (IFNAR1 & IFNAR2) genes among subjects affected with chronic hepatitis C, who have treated with IFN and RBV, and also relationship between HCV genotypes and response to combination antiviral therapy. Peripheral blood mononuclear cells (PBMCs) were taken from whole blood of 61 patients affected with chronic hepatitis C who were treated with IFN and Ribavirin. Then, DNA was extracted from PBMCs and quality of DNA was assessed with Nanodrop finally two SNPs [Ex4-30G>C] and [Ivs1-4640 G>A] of IFN receptor genes (IFNAR1 and IFNAR2) were measured by TaqMan Real-Time PCR in ABi Prism 7900 system. Also to confirm the response rate to therapy, RNA was extracted then RT PCR was performed and final product was studied with gel electrophoresis and UV spectroscopy. Statistical analysis was performed using SPSS version 18.0 for Windows. The analysis of results from TaqMan SNP Genotyping has been shown that two SNPs (Ex4-30G>C and Ivs1-4640 G>A) of IFNAR1 and IFNAR2 didn't show any relationship with response to combined therapy in subjects affected with chronic hepatitis C who have treated with peg-IFN-α and Ribavirin. 61 patients complete the treatment period. 54 patients (%88/5) of them responded to treatment and 7 patients (%11/5) did not. Research and data analysis have shown that there is no significant relationship between sex (P=0 /7) and age (P=0 /2). But there is a relationship between genotype-3a and response to combined therapy of IFN-α and RBV (0/02). Studies have shown that gene polymorphisms in IVSS1-22G location of IFNAR1 gene had a relationship with IFN treatment response. But current study has shown that there is no significant relationship between two SNPs Ex4-30G>C and Ivs1-4640 G>A and response to IFN therapy. In continue we suggest that it would be better to use this technique to evaluate other SNPs in IFN genes.

Rapid low-cost detection of hepatitis C virus RNA in HCV-infected patients by real-time RT-PCR using SYBR Green I.

BACKGROUND: We intend to design and validate a low-cost assay for the detection of hepatitis C virus (HCV) RNA using rapid-cycle RT-PCR. The procedure is performed in a closed system with little risk of contamination allowing PCR and product identification to be performed within one or two hours. METHODS: A SYBR Green-based real-time RT-PCR for rapid detection of HCV. Amplicon synthesis was monitored continuously by SYBR Green I, which binds to double stranded DNA during PCR. The PCR products were identified by melting curve analysis. Standard sera with known concentrations of HCV RNA and 150 clinical samples were used to validate our assay. RESULTS: The minimum detection level of our assay was less than 50 IU/mL. The results on 100 plasma samples were comparable with commercial assays. CONCLUSIONS: This method is useful for rapid qualitative detection of HCV infection and particularly suitable for routine diagnostic applications.

Mutations in the E2 and NS5A regions in patients infected with hepatitis C virus genotype 1a and their correlation with response to treatment.

Heterogeneity of subgenomic regions of hepatitis C virus (HCV) may be associated with response to interferon (IFN) therapy. The amino acid sequences of the PKR/eIF-2α phosphorylation homology domain (pePHD), IFN sensitivity determining region (ISDR), PKR binding domain (PKRBD), and variable region 3 (V3) were studied in 19 patients before and after 4 weeks of treatment. All patients were infected with HCV genotype 1a and were treated with pegylated-IFN and ribavirin. Thirteen patients achieved sustained viral response (responders) and six failed to clear viral RNA (nonresponders). The amino acid sequences in the pePHD and ISDR were identical in responders and nonresponders. However, amino acid substitution at position 2252 of PKRBD was significantly different between responders and nonresponders (P = 0.044). A larger number of mutations were observed in the V3 region of responders (P < 0.001). In this region, the amino acid in position 2364 differed between responders and nonresponders (responders: aspartic acid and serine, nonresponders: asparagine, P = 0.018). The amino acid sequences in the regions which were studied did not change after 4 weeks of treatment. It is concluded that the presence of specific amino acids in position 2252 of PKRBD and position 2364 of V3 might be associated with clinical response to IFN.