Catalase epitopes vaccine design for Helicobacter pylori: A bioinformatics approach

Bioinformatics tools are helpful for epitopes prediction directly from the genomes of pathogens in order to design a vaccine. Epitopes are sub-sequences of proteins (8 to 10 mer peptides) which bind to MHC to interact with the T cell receptors and stimulate immune responses. Finding a suitable vaccine against Helicobacter pylori is necessary, because of high prevalence of the infection (25 to 90%). Moreover, this bacteria has been classified as a grade I carcinogen by WHO since 1994. Catalase, an important enzyme in the virulence of H. pylori, could be a suitable candidate for vaccine design because it is highly conserved, which is important for the survival of H. pylori; it is expressed in high level and it is exposed on the surface of the bacteria. In this study, we designed epitope-based vaccine for catalase specific regions of H. pylori by means of immunobioinformatic tools. H. pylori (26695) catalase has been compared with human catalase in order to select specific regions. Afterwards, epitopes of catalase were determined by propred software. Among predicted epitopes, three epitopes were selected including, MVNKDVKQTT, VLLQSTWFL and FHPFDVTKI. Three candidates out of 51catalase antigen epitopes had the highest score for reactivating with MHC II MHC in propred software. The candidate epitopes for vaccine design should be rather a composition of considering epitopes: MVNKDVKQTTKKVLLQSTWFLKKFHPFDVTKI. In this manner, 39 of 51 alleles of MHC class ІІ were involved and stimulated T-cell responses. We believe prediction of catalase epitopes by the immunoinformatics tools would be valuable for developing new immuoprophylatic strategy against H. pylori infection.Key words: Helicobacter pylori, catalase, epitopes

Evaluation of various staphylococcal cassette chromosome mec (SCCmec) types in staphylococcus epidermidis invasive strains from hospitalized patients in Iran Valutazione di tipi diversi di cassetta cromosomica stafilococcica mec (SCCmec) in ceppi invasivi di Staphylococcus epidermidis isolate da pazienti ospedalizzati in Iran

Staphylococcus epidermidis is known to be a major cause of nosocomial infections particularly in catheter-associated bacteraemia, prosthetic valve endocarditis (PVE) and immunocompromised patients in different health care units. The emergence of multidrug-resistant strains, especially to β-lactam antibiotics such as methicillin, has increased the mortality due to S. epidermidis. A kind of low affinity penicillin-binding protein (PBP2α), which is encoded by the mecA gene that is located in the staphylococcal cassette chromosome mec (SCCmec), mediates the resistance to methicillin. The aim of this study was to investigate the prevalence of SCCmec types and evaluate the antibiotic profile assay in invasive strains isolated from clinical samples. The study focused on invasive strains, determining the antimicrobial resistance profile, designing new primers for detection of the mecA gene and SCCmec typing with the multiplex PCR method. By using the PCR molecular test, 87.1 of all isolates were found to be positive for the mecA gene. In SCCmec typing, different types (I-V) were identified, in which SCCmec type I was detected in 3 isolates, SCCmec type II in 5 isolates, SCCmec type III in 22 isolates, SCCmec type IV in 27 isolates and SCCmec type V was distinguished in 4 isolates. Since coagulase- negative staphylococci are reported as a major cause of hospital infections, molecular typing methods like SCCmec typing would be a helpful method to control and prevent bacterial infections. © 2015, EDIMES Edizioni Medico Scientifiche. All rights reserved

Phylogenetic analysis of prevalent tuberculosis and non-Tuberculosis Mycobacteria in Isfahan, Iran, based on a 360 bp sequence of the rpoB gene

Background: Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3 - 100), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation. Objectives: In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran. Materials and Methods: From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software. Results: Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50 were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98 and M. gordonae in another cluster with a bootstrap value of 90. In the fast-growing group, one cluster with a bootstrap value of 89 was defined, including all fast-growing members present in this study. Conclusions: The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85 - 100); the resulting tree has high validity. � 2016, Ahvaz Jundishapur University of Medical Sciences

In-vitro evaluation of miR-101-5P effect on herpes simplex virus replication

Background: Herpes simplex virus type 1 (HSV-1) is known worldwide for its serious disease and a kind of infection that involves nervous system throughout human lifelong. HSV-1 infection is much more considerable in immunocompromised patients and due to the growing resistance to its main drug, acyclovir, alternative treatments are required. MicroRNAs (miRNAs) regulate host and viral gene expression, post-transcriptionally. One previous study has shown that mir-101-3p expression may play role in HSV-1-infected cells. Methods: In this study, synthesized mimic hsa-miR-101-5p was transfected to HSV-1-infected Hela cells to observe its effect on HSV-1 replication via microscopic observation. Findings: Hela cells transfected by hsa-miR-101-5p produced less viral progeny, and expressed less cytopathic effects. Conclusion: Considering the effect of hsa-miR-101 in suppressing HSV-1 replication without affecting cell viability, this achievement can give us new insights in treatment of HSV-1 infection. © 2018, Isfahan University of Medical Sciences(IUMS). All rights reserved

The effect of miRNA mimic hsa-miR-7704 on in-vitro replication of herpes simplex virus type 1

Background: Herpes simplex virus type 1 (HSV-1) infections are of the most common diseases in human population. HSV-1 can cause subclinical to severe diseases, especially in immunocompromised patients. There are few anti-herpes drugs for treatment of HSV-1 infection. Acyclovir is one of the most important drugs. The extensive use of this drug has led to the development of resistant strains. Therefore, development of new anti-herpes drugs with different mechanisms is noticeable. This study aimed to use microRNAs as a novel method for inhibiting HSV-1 infection. Methods: Synthesized miRNA mimics hsa-miR-7704 (miR-SX1) were transfected into Hela cells, and then infected with HSV-1. Cellular morphological changes were observed 24 hours post-infection by inverted microscope, and photographed. Viral titers were measured using 50 tissue culture infective dose (TCID 50 ) method. Findings: miR-SX-1-transfected cells produced low-titer HSV-1, without affecting cell viability. Conclusion: The data suggest that miR-SX1 inhibits HSV-1 replication, and may provide an alternative mechanism to prevent HSV-1 infection. © 2018, Isfahan University of Medical Sciences(IUMS). All rights reserved

Inhibition of herpes simplex virus type 1 replication by novel hsa-miR-7704 in vitro

Herpes simplex virus type 1 (HSV-1) infections are one of the most common diseases in human population. HSV-1 causes subclinical, mild to severe diseases, especially in immunocompromised patients. Acyclovir has been used to reduce manifestations of HSV-1 infections. The extensive use of this drug has led to the development of resistant strains. Thus, designing a novel anti-herpes drug with different mechanisms of action is urgently needed. Cellular microRNAs (miRNAs) have direct antiviral effects in addition to their regulatory functions. In this study we used a novel miRNA (hsa-miR-7704), expressed in macrophages, to inhibit HSV-1 lytic infection in HeLa cells. Synthesized hsa-miR-7704 mimics were transfected into HSV-1 infected HeLa cell. The inhibitory effects of the miRNA were evaluated by plaque assay, real time polymerase chain reaction and the viral titers were measured by the 50 tissue culture infective dose (TCID 50 ). The viral titer and cell cytopathic effect were dramatically decreased in HeLa cells transfected with hsa-miR-7704 (50 and 100 nM), compared with HSV-1 infected cells alone or transfected with the mock miRNA control. These results suggest that hsa-miR-7704 inhibits HSV-1 replication efficiently in vitro. This may provide an alternative mechanism to prevent HSV-1 infections. © 2019 Medknow Publications.All rights reserved

Biological aspects of kilka (age, growth, feeding and reproduction) in southern of Caspian Sea

In the changing environmental of the Caspian Sea specifically pelagic zone following the introduction of the comb jelly Mnemiopsis leidyi has been continued ,particularly kilka catch ,biological characteristic and feeding . In this investigation which had been done in commercial catch regions (where discharged theirs catch) in three ports Babolsar ,Amirabad (in Mazandaran) and Anzali (in Guilan), estimated catch and catch per unit effort, the age structure of catch ,length- weight relationship, von Bertalanffy growth parameters, condition factor, sex ratios ,maturity stags ,age at first capture and spawning and feeding .The result shown that catch of kilka in Iranian coastal in 2006 decreased from 22300 ton to 16700 ton in 2008.But CPUE increased from1.7 ton (Vessel ×Night) to 2.5 ton at that time due to dropped effort .The length frequency of kilka is close and the juvenile fish did not see in catch as increased the length mean (P>0.000).The age frequency had the same situation as fish low than 2 years did not see for anchovy and bigeye ,so collapse juvenile stock cause poor recruitment in the species .The parameters of the von Bertalanffy growth curve were For common kilka L_∞= 136.5mm k= 0.249y t0= 1.890y Q= 3.883; For bigeye kilka L_∞= 131.7mm k= 0.346 t0= 1.123y Q= 3.688; And for anchovy kilka L_∞= 148mm k= 0.375 t0= 1.243y Q= 3.814 The exploitation rate of anchovy, bigeye and common kilka were 0.51, 0.58 and 0.6 respectively. The highest of GSI recorded in May and March for common and bigeye and in Jul, Nov for anchovy kilka .Main prey was Acartia tonsa by anchovy and common kilka and Cypris balanus by bigeye kilka. We concluded that the ecological problem causes by Mnemiopsis leidyi as well as overfishing has been collapsed kilka stocks, particularly anchvy.so sustainable fisheries management and conservation biodiversity in the Caspian Sea are real challenges now

Characterization and isolation of microsatellite in Persian sturgeon (Acipenser persicus, Borodine, 1897)

In order to have a sustainable management on Persian sturgeon (Acipenser persicus) as a highly commercial species in the South Caspian Sea, we need to identify its population structure and the level as well as its conservation status in their natural habitat. To develop a conservation program for this all Caspian Sea' sturgeon species it requires knowledge of its genetic diversity using reliable molecular marker to study population genetic structure. For these purposes, an enriched library was prepared based on a modified biotin-capture method. Approximately 1800 positive clones were screened for microsatellites in an Acipenser persicus genomic library. Of these 350 positively hybridizing clones were sequenced, and 81 clones were identified as having microsatellites with adequate flanking regions. We developed and tested 68 microsatellite primer pairs for Persian sturgeon. Out of 68 primer pairs developed, 11 pairs resulted in poor or no amplification, 13 were ambiguous, 6 were monomorphic, 20 were tetrasomic and 18 were octosomic in Persian sturgeon. While none of the markers showed disomic inheritance in Persian sturgeon and Russian sturgeon (A. gueldenstaedtii). Several of the markers appeared useful for studies stellate sturgeon (A. stellatus), ship sturgeon (A.nudiventris) and beluga (Huso huso). Nearly all the polymorphic pattern for ship, stellate and beluga displayed the simple banding patterns characteristic of disomic loci, while those for Russian sturgeon displayed banding patterns characteristic of tetraploid or higher polyploid levels. These markers may prove useful in a variety of future sturgeon population genetic studies in the Caspian Sea

Quantitative evaluation and identification of fungi in Shahid Rajaeii Dam Lake, Mazandaran Province (Sari)

The present study is carried out to investigate the fungal species present in water of Shahid Rajaeii damlake in Sari, (Mazandaran province). Samples were taken from five stations including, Station 1: Input of Shirinrud river, station 2: Input of Sefidrud river, Station 3: The confluence of the two branches, Station 4: dam crest and stations 5: Output dam from June to February 2012. Every sample was diluted by sterile saline (10-1 and 10-2) and 0.5 mL from each dilution was cultured on SD and incubated at 27-30°C for 3-5 days. Finally, the number of colonies wasrecorded as (colony forming unit = CFU) per 100 mL. Identification of fungal agents were conducted by slide culture preparation and stained in lacto-phenol blue. The results showed that in August and February were significantly highest and lowest rates of fungal colonies were isolated from water in different stations respectively. Moreover, the number of fungal colonies in the crown and the output was significantly higher than other stations. The frequency of identified fungi were: Aspergillus species (31.4%), various types of yeast (mainly Candida) (24.2%), Penicillium sp. (19.3%), Cladosporium sp.(10.3%), Mucor sp. (5.4%), Fusarium sp. (2.9%), sterile hype (2.8%), Alternaria sp. (2.3%) and Paecilomyces sp. (1.4%)

Stock assessment of sturgeon fishes in the southern part of Caspian Sea (Iranian water)

The marine survey for sturgeon stock assessment was conducted in summer, winter and spring in the years 2006 and 2009 to estimate the relative and absolute abundance and percentage composition of each species in the Guilan, Mazandaran and Golestan Provinces. This survey was carried out in the Iranian waters of the Caspian Sea on board the Sisara2 and Guilan vessels using trawl nets at 2-100 m depths. Trawling was carried out in 85 stations that were selected using a stratified random design. The number of stations in each scope was based on the area of the scope in terms of the total area. Trawling and sampling in shallow water up to 10 m were carried out using 9 m trawl nets whereas 24.7 m trawl nets were used for depths more than 10 m. Trawl surveys were carried out in the daytime. Trawling velocity was kept at 2.5-3 kts and trawls lasted half an hour in order to calculate abundance, and biomass of sturgeons using the swept area method. Catch per unit area (CPUA) in the winter 2006 survey was 3853 specimens nm^2 , in the summer and winter 2007 survey was 1854 , 2912 specimens nm^2 at depths less than 10 m respectively . CPUA for sturgeons in spring 2008 survey was 2103 specimens nm2 at depths less than 10 m and 393 specimens nm2 at depths greater than 10 m (10-100 m depth). These values in the winter 2008 survey dropped to 44 specimens nm^2 at depths at depths above 10 m. CPUA for sturgeons in the spring 2009 survey was 300 specimens nm^2 at depths less than 10 m and 307 specimens nm^2 at depths greater than 10 m. In all the surveys conducted CPUA for A. persicus was higher than that for the other sturgeon species. Based on the calculations carried out in the marine survey in winter 2006 the estimated absolute abundance for sturgeons was about 2977.363 thousand. The total biomass of sturgeon was estimated as 131.713 tons. In the summer 2007 survey total abundance was estimated 1432.398 thousand, and total biomass of sturgeons was estimated at about 312.161 tons. In the winter 2007 survey total abundance for sturgeons was estimated at about 2250.105 thousand, and total biomass was estimated 578.08 tons. In the spring 2008 survey total abundance was estimated at about 3002.832 thousand. The total biomass was estimated at about 2533.318 tons .In the winter 2008 survey total abundance was estimated at about 152.722 thousand, and total biomass in winter 2008 was estimated 170.540 tons. Total abundance in spring 2009 survey was 1310.232 thousand and total biomass was estimated at 2019.tons. Investigation of stomach content of sturgeon Acipenser persicus caught under 10m depth in 2006 to 2007 surveys showed that there is significant difference in the consumed food. Polychaeta is the major food consumed and crustacean an the minor one(P>0.05).Also no new types of food( such as bony fishes or benthic) have been observed in food chain of Acipenser persicus only the food consumption rate has been related to the season of year and increases or decreases in warm or cold seasons, respectively For physiological study and determination of sexual maturation stages in sturgeon,119 gonad sampling prepared. The results showed that 63 % of fishes were females and 37 % of them were males. Gill microscopic study shows complications such as hyperplasia, curvature, adhesion, embowed, shorting and lengthen of secondary filaments and fraught bloody. Microscopic study on liver indicates signs of cloudy inflammation, fatty degeneration, dispersion of billed secretions and cell atrophy. The population genetic structure of Persian sturgeon (Acipenser persicus) in Sefidrood and Gorganrood rivers watershed analyzed based on microsatellite markers during sturgeons assessment in 2006-2008. Results showed that Acipenser persicus in two region of south part of Caspian Sea are two independent populations