Engineered PUF proteins: New flexible toolkits to target the replication of RNA viruses

Aim: The RNA recognition code of an RNA-binding protein known as Pumilio/FBF (PUF) protein was reprogrammed in order to provide binding to internal ribosome entry site (IRES) of hepatitis C virus (HCV) genome. Materials & methods: The ability of the modified protein to repress IRES-dependent translation was analyzed by dual-luciferase reporter assay, cell viability assay, cell cytotoxicity assay and anti-HCV assay. Results: The modified protein was able to reduce reporter gene expression (>30) and HCV viral load (>98) and reduced HCV-induced cytotoxicity to the level observed in uninfected cells. Conclusion: Our results can set the stage for using modified PUFs for interfering with critical steps such as replication and translation in virus life cycle, especially RNA viruses. © 2021 Future Medicine Ltd

Ballast Stabilization with Polyurethane for Use in Desert Areas

Sand dune accumulation in the railways passing through desert areas leads to ballast softening and settlement, which is one of the major challenges in the ballast maintenance operation. In this regard, ballast infilling with polyurethane could be mentioned as a novel solution that has been less attentional in previous studies. In this matter, in present study using a domestic cost-effective polyurethane, the ballast stabilization has been accomplished and the relevant shear strength parameters have been investigated via a series of large-scale direct shear tests. Since the utilized polyurethane has composed of two different components, in the first stage, the best weight ratios of components have been investigated via a series of compression tests. In this matter, the ratio of 1.5 units polyol to 1 unit isocyanate has been adopted as the best composition. Then, the resulting polyurethane was injected into the ballast to perform large-scale direct shear tests. According to the measurement results, the maximum shear stress, the internal friction angle, and the cohesion coefficient increased by 109%, 9.5%, and 162.5% with respect to the non-stabilized ballast (NSB), respectively. In addition, the dilation angle decreased by 66.4% with the injection of polyurethane into the ballast. Hence, the results indicate increased shear strength and lateral track resistance in the presence of polyurethane, which can prevent lateral deflection and improve track safety. In other words, the mentioned polyurethane has improved the shear parameters of the ballast more significantly than other polyurethanes and has shown its performance in increasing the bearing capacity

High level of resistance to metronidazole and clarithromycin among Helicobacter pylori clinical isolates in Qazvin province, Iran

resistance. We aimed to investigate the prevalence and mechanism of antibiotic resistance to metronidazole and clarithromycin in H. pylori isolates collected from patients with gastrointestinal symptoms in Qazvin, Iran. In this cross-sectional study, antibiotic susceptibility testing to clarithromycin and metronidazole was performed among 80 clinical strains isolated from H. pylori-positive dyspeptic patients referred to Qazvin hospital from July 2018 to November 2018. Polymerase chain reaction (PCR) and sequencing tests were performed to determine the type of mutations in the rdxA gene in metronidazole-resistant isolates, and the 23SrRNA gene in clarithromycinresistant isolates. Thirteen (40.6%) and Twenty-one (65.6%) isolates were resistant to clarithromycin and metronidazole, respectively. 37.5% and 59.4% of clarithromycin and metronidazole resistant isolates had MIC>256. In clarithromycin-resistant isolates, mutations in the 23SrRNA gene was seen at A2143G (15.6%), A2142G (9.4%), C2195T (6.3%), C2244T (3.1%), and G2212A (3.1%) locations. In one isolate, three simultaneous mutations were recorded in locations A2143G, G2110A, and C2121T. Mutations in the rdxA gene in metronidazole-resistant isolates, were missense. High resistance to metronidazole and clarithromycin antibiotics were seen in H. pylori isolates in Qazvin province. This is the first report of new mutation sites G2212A, G2110A, and C2121T on the 23SrRNA gene in clarithromycin-resistant isolates. It is necessary to evaluate the current situation in terms of resistance and identify the mechanisms involved in its occurrence for the successful treatment of infections caused by this organism

High level of resistance to metronidazole and clarithromycin among Helicobacter pylori clinical isolates in Qazvin province, Iran

The treatment of patients with Helicobacter pylori infection has many limitations, especially because of antibiotic resistance. We aimed to investigate the prevalence and mechanism of antibiotic resistance to metronidazole and clarithromycin in H. pylori isolates collected from patients with gastrointestinal symptoms in Qazvin, Iran. In this cross-sectional study, antibiotic susceptibility testing to clarithromycin and metronidazole was performed among 80 clinical strains isolated from H. pylori-positive dyspeptic patients referred to Qazvin hospital from July 2018 to November 2018. Polymerase chain reaction (PCR) and sequencing tests were performed to determine the type of mutations in the rdxA gene in metronidazole-resistant isolates, and the 23SrRNA gene in clarithromycinresistant isolates. Thirteen (40.6%) and Twenty-one (65.6%) isolates were resistant to clarithromycin and metronidazole, respectively. 37.5% and 59.4% of clarithromycin and metronidazole resistant isolates had MIC>256. In clarithromycin-resistant isolates, mutations in the 23SrRNA gene was seen at A2143G (15.6%), A2142G (9.4%), C2195T (6.3%), C2244T (3.1%), and G2212A (3.1%) locations. In one isolate, three simultaneous mutations were recorded in locations A2143G, G2110A, and C2121T. Mutations in the rdxA gene in metronidazole-resistant isolates, were missense. High resistance to metronidazole and clarithromycin antibiotics were seen in H. pylori isolates in Qazvin province. This is the frst report of new mutation sites G2212A, G2110A, and C2121T on the 23SrRNA gene in clarithromycin-resistant isolates. It is necessary to evaluate the current situation in terms of resistance and identify the mechanisms involved in its occurrence for the successful treatment of infections caused by this organism

Nucleotide identity and variability among different Pakistani hepatitis C virus isolates

<p>Abstract</p> <p>Background</p> <p>The variability within the hepatitis C virus (HCV) genome has formed the basis for several genotyping methods and used widely for HCV genotyping worldwide.</p> <p>Aim</p> <p>The aim of the present study was to determine percent nucleotide identity and variability in HCV isolates prevalent in different geographical regions of Pakistan.</p> <p>Methods</p> <p>Sequencing analysis of the 5'noncoding region (5'-NCR) of 100 HCV RNA-positive patients representing all the four provinces of Pakistan were carried out using ABI PRISM 3100 Genetic Analyzer.</p> <p>Results</p> <p>The results showed that type 3 is the predominant genotypes circulating in Pakistan, with an overall prevalence of 50%. Types 1 and 4 viruses were 9% and 6% respectively. The overall nucleotide similarity among different Pakistani isolates was 92.50% ± 0.50%. Pakistani isolates from different areas showed 7.5% ± 0.50% nucleotide variability in 5'NCR region. The percent nucleotide identity (PNI) was 98.11% ± 0.50% within Pakistani type 1 sequences, 98.10% ± 0.60% for type 3 sequences, and 99.80% ± 0.20% for type 4 sequences. The PNI between different genotypes was 93.90% ± 0.20% for type 1 and type 3, 94.80% ± 0.12% for type 1 and type 4, and 94.40% ± 0.22% for type 3 and type 4.</p> <p>Conclusion</p> <p>Genotype 3 is the most prevalent HCV genotype in Pakistan. Minimum and maximum percent nucleotide divergences were noted between genotype 1 and 4 and 1 and 3 respectively.</p

第711回 千葉医学会例会・第20回 佐藤外科例会 32.

<p>It obtained by maximum likelihood method using HKY+<i>Г</i>+I as nucleotides' substitution model. Triangleshows the position of cluster C which is detailed in (A). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162492#pone.0162492.g001" target="_blank">Fig 1</a> legend for more details.</p

A Novel PSOGSA_SQP Algorithm for Solving Optimal Power Flow (OPF) Problem Based on Specific Switching Condition

Abstract In this paper, PSOGSA_SQP novel hybrid algorithm is proposed to solve the optimal power flow (OPF) problem. Employing the proposed method aims at optimally adjusting control variables and increasing speed. The performance of the proposed method is studied on a standard system introduced in IEEE standards with 30 buses and specific objective functions which seek to minimize generator fuel costs, voltage stability and voltage profile improvement in different modes. Simulation results certify that this algorithm is faster than other methods such as PSO, GSA, GA, in view of using the SQP classical gradient-based method and its combination with PSOGSA intelligent method. We also propose a new switching method to switch from intelligent optimization method to SQP. This algorithm minimizes cost function value by accurately adjusting control variables

Polycyclic Aromatic Hydrocarbon Contamination Levels in Collected Samples From Vicinity of a Highway

Tehran as the biggest city of Iran with a population of more than 10 millions has potentially high pollutant exposures of gas oil and gasoline combustion from vehicles that are commuting in the highways every day. The vehicle exhausts contain polycyclic aromatic hydrocarbons, which are produced by incomplete combustion and can be directly deposited in the environment. In the present study, the presence of polycyclic aromatic hydrocarbons contamination in the collected samples of a western highway in Tehran was investigated. The studied location was a busy highway in Tehran. High performance liquid chromatography equipped with florescence detector was used for determination of polycyclic aromatic hydrocarbons concentrations in the studied samples. Total concentration of the ten studied polycyclic aromatic hydrocarbons compounds ranged from 11107 to 24342 ng/g dry weight in the dust samples and increased from 164 to 2886 ng/g dry weight in the soil samples taken from 300 m and middle of the highway, respectively. Also the average of ∑ PAHs was 1759 ng/L in the water samples of pools in parks near the highway. The obtained results indicated that polycyclic aromatic hydrocarbons contamination levels were very high in the vicinity of the highway

Hepatitis C Virus Infection and HCV Genotypes of Hemodialysis Patients

&quot;nBackground: To evaluate the prevalence of hepatitis C by antibody testing, HCV-RNA detection by PCR and relative risk fac&amp;shy;tors of HCV infection among HD patients and staff members in Markazi Province/Iran. The other purpose was to deter&amp;shy;mine genotypes of HCV in this population.&quot;nMethods: The study group consisted of 204 HD patients and 47 staff members from all 9 dialysis centers in Markazi Prov&amp;shy;ince, Iran. Anti-HCV antibodies were tested using a third generation ELISA and confirmed by RIBA. HCV RNA was deter&amp;shy;mined by RT-PCR and genotyping was performed by a reverse hybridization assay (LiPA).&quot;nResults: The overall prevalence of HCV (HCV antibody and HCV-RNA) was 5.4%. Female sex (P= 0.019), duration of dialy&amp;shy;sis (P= 0.003) and kidney transplant (P= 0.049) were significantly correlated with HCV infection. The predominant sub&amp;shy;type was HCV-1a, detected in 4(50%) of the 8 HD patients. Genotype 4, 3a and 1b were found in 2(25%), 1(12.5%) and 1(12.5%) patients respectively. &amp;nbsp;The prevalence of anti-HCV among staff members of HD units was 0%.&quot;nConclusion: The presence of anti HCV positive patients who had never been transfused, high prevalence of genotype 4 in this population, duration of HD as a risk factor for HCV positivity and non significant association between blood transfu&amp;shy;sion and HCV infection suggest nosocomial transmission of the virus in dialysis units that needs to be confirmed by phyloge&amp;shy;netic analysis of subgenomic regions of HCV. HD staff members dose not seem to be at increased risk of hepatitis C de&amp;shy;spite the frequent blood exposure and lack of strict adherence to universal infection control precautions. &quot;n&amp;nbsp