Bovine viral diarrhea virus (BVDV) is the cause of bovine viral diarrhea disease, one of the most economically important livestock diseases worldwide. The majority of BVD disease control programs rely on the detection and then elimination of persistent infection (PI) cattle, as the continuing source of disease. The main purpose of this study was to design and develop an accurate G-quadruplex-based aptasensor for rapid and simple detection of BVDV-1. In this work, we utilized in silico techniques to design a G-quadruplex aptamer specific for the detection of BVDV-1. Also, the rationally designed aptamer was validated experimentally and was used for developing a colorimetric biosensor based on an aptamer-gold nanoparticle system. Firstly, a pool of G-quadruplex forming ssDNA sequences was constructed. Then, based on the stability score in secondary and tertiary structures and molecular docking score, an aptamer (Apt31) was selected. In the experimental part, gold nanoparticles (AuNPs) with an average particle size of 31.7 nm were synthesized and electrostatically linked with the Apt31. The colorimetric test showed that salt-induced color change of AuNPs from red to purple-blue occurs only in the presence of BVDV-Apt31 complex, after 20 min. These results approved the specificity of Apt31 for BVDV. Furthermore, our biosensor could detect the virus at as low as 0.27 copies/ml, which is an acceptable value in comparison to the qPCR method. The specificity of the aptasensor was confirmed through cross-reactivity testing, while its selectivity was confirmed through plasma testing. The sample analysis showed 90% precision and 94% accuracy. It was concluded that the biosensor was adequately sensitive and specific for the detection of BVDV in plasma samples and could be used as a simple and rapid method on the farm. © 2024 Rabiei et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Microbial Pathogenesis (10961208)196
Today, many infections in plants are related to biofilm-developing bacteria. These infections can result in severe agricultural losses. Thus, this study aims to investigate the synergistic antibiofilm activity of Thymus vulgaris extract on the inherent antibacterial properties of ZnO nanoparticles against Erwinia amylovora and Pseudomonas syringae pv. syringae. Additionally, to gain insight into the molecular mechanisms of phytocompounds’ antibacterial activity, the molecular interactions of T. vulgaris phytochemicals with the TolC protein and TonB-dependent siderophore receptor were investigated through in-silico studies. Green-synthesized ZnO NPs (ZnO@GS) and chemically synthesized ZnO (ZnO@CHS) were evaluated using XRD and SEM techniques, showing a crystalline structure for both powders with average sizes of 50, and 40 nm, respectively. According to FT-IR and EDS spectroscopy, ZnO@GS was covered with thyme extract. Based on the in vitro results, all samples of ZnO NPs exhibited considerable antibacterial activity against both bacteria. At the same time, thyme aqueous extract alone proved considerably less effective at all tested concentrations. Compared to ZnO@CHS and thyme extract, the antibacterial efficacy of ZnO@GS against E. amylovora (MIC = 512 μg/mL) and P. syringae pv. syringae (MIC = 256 μg/mL) was significantly improved upon surface covering with thyme phytocompounds. Moreover, their antibiofilm properties were enhanced by almost 20 % compared to ZnO@CHS. In addition, molecular docking investigations showed that most of the phytocompounds could form stable interactions with the TonB-dependent siderophore receptor (P. syringae) plug domain and the TolC (E. amylovora) external channel. In vitro and in silico studies demonstrate that using the green approach for synthesizing ZnO NPs via thyme extract can notably boost its antibacterial and antibiofilm effects on the tested phytopathogenic bacteria. © 2024 Elsevier Ltd
Microbial Pathogenesis (10961208)194
Cancer is one of the main causes of death in the world. Resistance to anticancer treatments in patients with advanced solid tumors leads to new treatments. Therefore, more alternative anticancer methods have been found over time with greater specificity against tumor cells and with less or no adverse effects on normal cells. Bacterial spores of obligate anaerobes exclusively germinate in the hypoxic/necrotic areas and not in the well oxygenated areas of the body. This unique phenomenon has been exploited in using bacterial spores as a remedy for cancer. Bacterial toxins also play a significant role in either directly killing tumor cells or altering the cellular processes of the tumor cells which ultimately leads to the inhibition and regression of the solid tumor. In the microbial environment, pathogens such as Staphylococcus aureus, Bacillus cereus, or Streptococcus pyogenes produce hemolysin. This protein is used as an anti-cancer protein. To identify the production of hemolysin by bacteria, which can destroy cancer cells more effectively, different bacterial strains were first cultured in blood agar culture medium. The Strains that completely lysed red blood cells, creating transparent zones, were selected for further investigation. Then, to find out which strains have more ability to lyse red blood cells, the qualitative method of halo diameter measurement was used. Also, using quantitative methods, hemolysin strength in microtubes was determined compared to control samples. The results of the hemolysis in the microtube and the qualitative test results showed similar results. In the next step, the cell viability test was performed with the partially purified proteins. Then, bioinformatics studies such as secondary structure investigation, physicochemical properties, pseudo amino acid composition, and molecular docking were performed. The results of molecular docking showed that the hemolysin protein has the highest affinity for the cholesterol of the cytoplasmic membrane, respectively, of Bacillus subtilis, Bacillus cereus, and Staphylococcus aureus bacteria which play a significant role in either directly killing tumor cells or altering the cellular processes of the tumor cells which ultimately leads to the inhibition and regression of the solid tumor. © 2024 Elsevier Ltd
PLoS ONE (19326203)19(6 June)
The development of a cancer vaccine has become an essential focus in the field of medical biotechnology and immunology. In our study, the NY-SAR-35 cancer/testis antigen was targeted to design a novel peptide vaccine using bioinformatics tools, and BALB/c mice were used to evaluate the vaccine’s immunological function. This evaluation involved assessing peptide-specific IgG levels in the serum via ELISA and measuring the levels of IFN-γ, IL-4, and granzyme B in the supernatant of cultured splenocytes. The final vaccine construct consisted of two T lymphocyte epitopes linked by the AAY linker. This construct displayed high antigenicity, non-allergenicity, non-toxicity, stability, and ability to induce IFN-γ and IL-4. It showed stable dynamics with both human MHC-I and II molecules, as well as mouse MHC-II molecules, and revealed strong Van der Waals and electrostatic energies. Emulsifying our peptide vaccine in incomplete Freund’s adjuvant resulted in a remarkable increase in the levels of IgG. The splenocytes of mice that received the combination of peptide and adjuvant displayed a noteworthy increase in IFN-γ, IL-4, and granzyme B secretion. Additionally, their lymphocytes exhibited higher proliferation rates compared to the control group. Our data demonstrated that our vaccine could stimulate a robust immune response, making it a promising candidate for cancer prevention. However, clinical trials are necessary to assess its efficacy in humans. © 2024 Samman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Iranian Journal Of Science (27318095)48(1)pp. 9-16
Serine proteases are an essential and immensely diverse group of enzymes found in many different organisms, from mammals to viruses. Alkaline serine proteases (ASPs) are a type of serine protease that exhibit their highest activity levels in alkaline conditions. These enzymes play a critical role across a wide range of industries, providing immense value and benefits. ASPs are produced mainly by bacteria and fungi on industrial scales. The present study involved an analysis of various sequences of alkaline serine proteases derived from fungi and bacteria. The analytical approach employed encompassed the assessment of the pseudo amino acid composition (PseAAC), the tripeptide composition (TPC), physicochemical properties, secondary structures, and conserved motifs. Motif discovery and analysis showed that a considerable majority of bacterial alkaline serine protease sequences (over 94%) and fungal alkaline serine protease sequences (99%) in the dataset were associated with the subtilisin-like serine protease superfamily. This finding highlights the prevalence of this particular superfamily in alkaline serine protease sequences and provides valuable insight into the evolutionary relationships between different protease families. Based on the results of the study, the utilization of PseAAC and TPC techniques was successful in categorizing fungal and bacterial ASPs into separate groups. This was made possible by precise predictive models generated using machine learning algorithms. Bacterial and fungal ASPs had no significant differences in amino acid composition, ProtParam features, and GORIV secondary structure prediction outcomes. This underscores the importance of TPC and PseAAC concepts in accurately clustering and predicting ASP sequences. © The Author(s), under exclusive licence to Shiraz University 2024.
Probiotics have poor gastrointestinal delivery because they lose their viability during intestinal passage. Microencapsulation has a significant effect on the survival of probiotic bacteria. This study aimed to synthesize chitosan-alginate nanoparticles and encapsulate Bacillus coagulans NBRC-12583 and Enterococcus faecium MGFR1 in alginate (Alg), chitosan (Cht) and inulin (Inu) by micro- and nano-encapsulation to investigate the viability of encapsulated strains in simulated gastrointestinal condition. The survival of free and encapsulated bacteria was studied for 120 min. The population of B. coagulans encapsulated in Cht-Alg only decreased by 0.86 log CFU, while that of E. faecium encapsulated in Cht-Alg nanoparticles only decreased by 0.27 log CFU. Treated with simulated intestinal fluid, B. coagulans and E. faecium populations decreased by 1.03 and 0.17 log CFU, respectively. E. faecium microencapsulated in Cht-Alg and Inu had a maximum encapsulation efficiency of 96.78%. E. faecium encapsulated in Cht-Alg nanoparticles and Inu was more viable than other encapsulated bacteria. Scanning electron microscopy was done to investigate the microcapsules' surface morphology, structure, internal cross-sectional view, and the zeta potential for the surface charge of Cht-Alg nanoparticles. The viability of the probiotic bacteria was enhanced significantly by microencapsulation and nanomaterial-based encapsulation within the chitosan-alginate and inulin matrix. © 2024
International Journal Of Molecular And Cellular Medicine (22519645)13(1)pp. 46-63
One of the burning issues facing healthcare organizations is multidrug-resistant (MDR) bacteria. P. aeruginosa is an MDR opportunistic bacterium responsible for nosocomial and fatal infections in immunosuppressed individuals. According to previous studies, efflux pump activity and biofilm formation are the most common resistance mechanisms in P. aeruginosa. The aim of this study was to propose new antimicrobial peptides (AMPs) that target P. aeruginosa and can effectively address these resistance mechanisms through in silico and in vitro assessments. Since AMPs are an attractive alternative to antibiotics, in vitro experiments were carried out along with bioinformatics analyses on 19 Nef peptides (derived from the HIV-1 Nef protein) in the current study. Several servers, including Dbaasps, Antibp2, CLASSAMP2, ToxinPred, dPABBs and ProtParam were used to predict Nef peptides as AMPs. To evaluate the binding affinities, a molecular docking analysis was performed with the HADDOCK web server for all Nef peptide models against two effective proteins of P. aeruginosa (MexB and PqsR) that play a role in efflux and quorum sensing. Moreover, the antibacterial and antibiofilm activity of the Nef peptides was investigated in a resistant strain of P. aeruginosa. The results of molecular docking revealed that all Nef peptides have a significant binding affinity to the abovementioned proteins. Nef-Peptide-19 has the highest affinity to the active sites of MexB and PqsR with the HADDOCK scores of -136.1 ± 1.7 and -129.4 ± 2, respectively. According to the results of in vitro evaluation, Nef peptide 19 showed remarked activity against P. aeruginosa with minimum inhibitory and bactericidal concentrations (MIC and MBC) of 10 µM and 20 µM, respectively. In addition, biofilm inhibitory activity was observed at a concentration of 20 µM. Finally, Nef peptide 19 is proposed as a new AMP against P. aeruginosa. © The Author(s). Publisher: Babol University of Medical Sciences This work is published as an open access article distributed under the terms of the Creative Commons Attribution 4.0 License (http://creativecommons.org/licenses/by-nc/4). Non-commercial uses of the work are permitted, provided the original work is properly cited.
Molecular Biology Research Communications (2322181X)13(4)pp. 183-191
L-asparaginase is a commercial enzyme with a wide variety of applications. Asparaginase is known as an anti-cancer agent that is effective for the treatment of certain lymphomas and leukemias by growth inhibition of human cancer cells. Additionally, asparaginase is used in the food industry in a pretreatment process to decrease the accumulation of carcinogenic acrylamide. In this paper, different aspects of bacterial and fungal asparaginases such as mass, hydrophobicity and hydrophilicity of pseudo amino acid composition (PseAAC), physicochemical properties, and structural motifs were studied, and ROC curve statistical analysis was used for the comparison. The results showed that none of the physicochemical properties of fungal and bacterial asparaginase could not be differed, except molecular weight and sequence length. MEME Suite analysis demonstrated that there was a motif that was specific for bacterial asparaginases. However, analysis based on the concept of PseACC indicated a differentiation line between fungal and bacterial asparaginases. In conclusion, although there was not any specific demonstration to separate the bacterial and fungal asparaginases in the case of physicochemical properties, PseAAC analysis can be an appropriate and usable method to differentiate between them. © (2024), (Shiraz University). All rights reserved.
Journal of Biomedical Materials Research - Part B Applied Biomaterials (15524973)112(2)
More than 70% of hospital-acquired urinary tract infections are related to urinary catheters, which are commonly used for the treatment of about 20% of hospitalized patients. Urinary catheters are used to drain the bladder if there is an obstruction in the tube that carries urine out of the bladder (urethra). During catheter-associated urinary tract infections, microorganisms rise up in the urinary tract and reach the bladder, and cause infections. Various materials are used to fabricate urinary catheters such as silicone, polyurethane, and latex. These materials allow bacteria and fungi to develop colonies on their inner and outer surfaces, leading to bacteriuria or other infections. Urinary catheters could be modified to exert antibacterial and antifungal effects. Although so many research have been conducted over the past years on the fabrication of antibacterial and antifouling catheters, an ideal catheter needs to be developed for long-term catheterization of more than a month. In this review, we are going to introduce the recent advances in fabricating antibacterial materials to prevent catheter-associated urinary tract infections, such as nanoparticles, antibiotics, chemical compounds, antimicrobial peptides, bacteriophages, and plant extracts. © 2024 Wiley Periodicals LLC.
Molecular Biology Research Communications (2322181X)12(3)pp. 117-126
Phospholipases, as important lipolytic enzymes, have diverse industrial applications. Regarding the stability of extremophilic archaea’s proteins in harsh conditions, analyses of unusual features of their proteins are significantly important for their utilization. This research was accomplished to in silico study of archaeal phospholipases’ properties and to develop a pioneering method for distinguishing these enzymes from other archaeal enzymes via machine learning algorithms and Chou’s pseudo-amino acid composition concept. The non-redundant sequences of archaeal phospholipases were collected. BioSeq-Analysis sever was used with Support Vector Machine (SVM), Random Forests (RF), Covariance Discrimination (CD), and Optimized Evidence-Theoretic K-nearest Neighbor (OET-KNN) as powerful machine learnings algorithms. Also, different Chou’s pseudo-amino acid composition modes were performed and then, 5-fold cross-validation was applied to the sequences. Based on our results, the OET-KNN predictor, with 96% accuracy, yields the best performance in SC-PseAAC mode by 5-fold cross-validation. This predictor also achieved very high values of specificity (95%), sensitivity (96%), Matthews’s correlation coefficient (0.92), and accuracy (96%). The present investigation yielded a robust anticipatory model for the archaeal phospholipase prediction utilizing the tenets PseAAC and OET-KNN machine learning algorithm. © This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).
Arabian Journal Of Chemistry (18785352)15(11)
Staphylococcus aureus is a common bacterial agent of biofilm formation in medical environments. The formed biofilm of this bacterium in bone tissue is one of the main causes of osteomyelitis, which is a serious health issue. Due to the importance of this infection after traumatic injuries or surgical intervention, it is necessary to develop a system that could release the antibiotics at the site of injury, specifically and gradually. The current study aimed to develop a nanosystem composed of single-stranded G-quadreplex DNA aptamer as the bio-recognition element, mesoporous silica nanoparticles (MSNs) as the carrier for gradual drug release, and Ampicillin as the cargo to be delivered to the site of infection. In silico methods were used to select an optimum binding aptamer against protein A of S. aureus. The binding of aptamer was confirmed via gel retardation assay, DLS, and Zeta potential analyses. The loading of the drug was confirmed by the FTIR method, and the drug release investigation showed almost 30 % of drug release via 48 h dialysis assay. The acquired results from the biofilm suppression assay indicated that this system provides a significant inhibitory effect against the S. aureus biofilm and has a high potential for the desired drug release to prevent the formation of biofilm, and could destroy the biofilm on the mice bone. The results of the MTT assay proved that this system does not pose a significant toxicity thread for MCF-7 cell viability, as a model for eukaryotic cells. In vivo studies are required to further confirm the efficacy of this system against S. aureus biofilm on bone. © 2022 The Authors
Zanjanchi, P.,
Asghari, S.M.,
Mohabatkar, H.,
Shourian, M.,
Shafiee ardestani, M. Journal of Nanobiotechnology (14773155)20(1)
Background: Inhibition of tumor angiogenesis through simultaneous targeting of vascular endothelial growth factor receptor (VEGFR)-1 and -2 is highly efficacious. An antagonist peptide of VEGFA/VEGFB, referred to as VGB3, can recognize and neutralize both VEGFR1 and VEGFR2 on the endothelial and tumoral cells, thereby inhibits angiogenesis and tumor growth. However, improved efficacy and extending injection intervals is required for its clinical translation. Given that gold nanoparticles (GNPs) can enhance the efficacy of biotherapeutics, we conjugated VGB3 to GNPs to enhance its efficacy and extends the intervals between treatments without adverse effects. Results: GNP–VGB3 bound to VEGFR1 and VEGFR2 in human umbilical vein endothelial (HUVE) and 4T1 mammary carcinoma cells. GNP–VGB3 induced cell cycle arrest, ROS overproduction and apoptosis and inhibited proliferation and migration of endothelial and tumor cells more effectively than unconjugated VGB3 or GNP. In a murine 4T1 mammary carcinoma tumor model, GNP–VGB3 more strongly than VGB3 and GNP inhibited tumor growth and metastasis, and increased animal survival without causing weight loss. The superior antitumor effects were associated with durable targeting of VEGFR1 and VEGFR2, thereby inhibiting signaling pathways of proliferation, migration, differentiation, epithelial-to-mesenchymal transition, and survival in tumor tissues. MicroCT imaging and inductively coupled plasma mass spectrometry showed that GNP–VGB3 specifically target tumors and exhibit greater accumulation within tumors than the free GNPs. Conclusion: Conjugation to GNPs not only improved the efficacy of VGB3 peptide but also extended the intervals between treatments without adverse effects. These results suggest that GNP–VGB3 is a promising candidate for clinical translation. Graphical Abstract: [Figure not available: see fulltext.] © 2021, The Author(s).
Aquaculture (00448486)548
White spot syndrome virus (WSSV) is one of the most threatening viral pathogens of shrimp worldwide. VP28, the major capsid protein of WSSV, is reported to play an essential role in the interaction with the host cells. Usually, the diagnostic test of WSSV is performed by one-step PCR, which is neither field-usable nor rapid enough. Therefore, the development of early diagnostic tests is imperative for the management of disease and to prevent huge economic losses. In this work, a rapid colorimetric aptasensor with high selectivity and sensitivity was introduced. First, a new ssDNA aptamer for the detection of WSSV was designed from a random pool of aptamer sequences based on the docking score and bioconjugate free energy, and then, evaluated experimentally. The designed aptamer was used to prepare an aptasensor conjugate gold nanoparticles (AuNPs) as a recognition element that increased the resistance of AuNPs to salt-induced aggregation. Therefore, the AuNPs with spherical morphology and average particle size of about 20 nm were synthesized for this reason. The results showed that the aptamer didn't attach to the other pathogens (i.e., IHHN and Vibrio harveyi) and healthy shrimp cells, and remained stable. Interestingly, the gray-blue color of aptasensor was seen only by the presence of WSSV, indicating the aptasensor assay showed good specificity to WSSV. The limit of detection (LOD) of the aptasensor was 104 copies of WSSV that could be detected only utilizing naked eyes. It was concluded that the designed aptamer had excellent potential for the detection of WSSV as a rapid visual colorimetric assay in aquaculture shrimp farmers. © 2021 Elsevier B.V.
RSC Advances (20462069)12(38)pp. 24876-24886
Streptococcus mutans is a commensal and opportunistic pathogen that causes several diseases by forming a biofilm in humans and animals in many areas such as nasopharyngeal, cardiac valves, lungs, and oral cavity. Biofilms are very important in prosthetic infections associated with medical implants. The use of nanoparticles is one of the evolving fields in biofilm targeting. Silver nanoparticles can be used for biofilm targeting due to their inherent antimicrobial properties. Hybridization of nanoparticles with small molecules increases their biological properties and makes them multifunctional. The present investigation aimed to design an appropriate silver nanoparticles-aptamer complex that binds to the surface receptors of streptococcal strains. For this reason, silver nanoparticles with particle sizes in a range of 50 to 70 nm were synthesized and connected to a designed aptamer with a streptavidin-biotin linker. Then, the effect of the complex was investigated on the S. mutans biofilm formed on the surface of a medical-grade titanium substrate. The silver nanoparticles-aptamer complex at a concentration of 100 μg mL−1 after 48 h inhibited 43% of the biofilm formation and degraded 63% of the formed biofilm. Also, the cell availability reached 96% and the complex was stable in cell medium culture for 360 min. It was concluded that this complex could be a good candidate for removing the formed biofilms on the surface of titanium implants. © 2022 The Royal Society of Chemistry.
Journal of Drug Delivery Science and Technology (17732247)71
The development of multifunctional nano-carriers with the ability of stimuli responsive controlled drug release can address many of the challenges of current cancer therapies. Graphene oxide (GO)-based nanomaterials with great specific surface area and oxygen-rich functional groups show desirable advantages for drug delivery systems. Therefore, in this research, GO sheets were functionalized by grafting hyperbranched polyglycerol- (HPG) through anionic ring-opening multi-branching polymerization (Anionic-ROMBP) of glycidol monomer. Then, magnetic nanoparticles (MNPs) were fabricated between the branches and on the surface of GO using the co-precipitation method (GO-HPG-MNPs). An anti-cancer model drug, curcumin (CUR), was loaded inside the nano-carrier via hydrophobic and π-π stacking interactions. After determining drug release pattern at weak acidic and physiological pH, the cytotoxicity of nano-carrier was investigated by MTT assay. FITC Annexin V/PI apoptosis detection kit was also applied to determine the method of cancer cells death. In addition to the in vitro studies, iATC-mISF bioinformatics server was used to predict the therapeutic and anatomical properties of CUR and its 75 derivatives. According to the results, GO-HPG-MNPs-(CUR) with negative surface charge (−49.4 mV) represented about 198% drug loading capacity and pH-responsive drug release. Results of MTT assay and flow cytometry confirmed cytotoxicity and apoptotic ability of GO-HPG-MNPs-(CUR) in cancer cells, while GO-HPG-MNPs (without drug) was biocompatible with no tangible toxicity. Moreover, for the first time, the conformity of MTT assay data and bioinformatics predictions exhibited the specific therapeutic/anatomical potential of CUR and about 51% of its derivatives on the nervous system. Thus, GO-HPG-MNPs-(CUR) can be suggested as a new type of functional nano-carrier in anti-cancer drug delivery and targeted cancer therapy. © 2022 Elsevier B.V.
Journal of Microbiology, Biotechnology and Food Sciences (13385178)11(3)pp. 1-5
COVID-19 has shown higher virulence compared to the previous coronavirus epidemics and has shown that it causes damages to the nervous system. In the present study, PrionW web server was used to predict the prion-like domains (PrLDs) in 15 structural and non-structural proteins of SARS-CoV, MERS-CoV and SARS-CoV-2. Among all of these proteins, the results demonstrated one PrLD with the sequence 951EDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQL1012, having an amyloid-core of 988GQQDGSEDNQTTTIQTIVEVQ1009 in the non-structural protein of SARS-CoV-2 with pWALTZ_Score of 59.9936. The sequence of SARS-CoV-2 polyprotein was further investigated by FoldIndex© tool, and a negative fold index was demonstrated at the site of predicted prion-like domain. Multiple sequence alignment of this region with non-structural proteins of SARS-CoV and MERS-CoV, showed that there is no sequence similarity between this predicted region and the corresponding regions of two other viruses. Considering the high similarity between polyproteins of SARS-CoV-2 and SARS-CoV, and their ability to affect the nervous system, it could be suggested that a potential PrLD might be added to SARS-CoV polyprotein. © 2021. All Rights Reserved.
Molecular Biology Research Communications (2322181X)10(4)pp. 171-178
SARS-CoV-2 is a member of β-genus of the coronavirus subfamily, alongside the virus that causes SARS (Severe Acute Respiratory Syndrome). As implied by their names, SARS-CoV-2 and SARS-CoV genome sequences have close kinship (about 79% genomic sequence similarity). In the current research, sequence-based physiochemical properties of RNA polymerase and membrane glycoprotein of SARS-CoV-2 and SARS-CoV were compared. In addition, impacts of substitution mutations on stability and glycosylation patterns of these proteins were studied. In comparison of physiochemical features of membrane and RNA polymerase proteins, only instability index of membrane protein was difference between SARS-CoV and SARS-CoV-2. Mutation analysis showed increase in stability of RNA polymerase and decrease in stability of membrane protein in SARS-CoV-2. Glycosylation pattern analysis showed glycosylation enhancement in both membrane and RNA polymerase proteins of SARS-CoV-2 in comparison to SARS-CoV. In conclusion, more glycosylation and stability of SARS-CoV-2 RNA polymerase could be one of the reasons of high pathogenicity property and host immune system evasion of SARS-CoV-2. © 2021. All Rights Reserved.
Informatics in Medicine Unlocked (23529148)26
Nucleic acid aptamers are short sequences of nucleic acid ligands that bind to a specific target molecule. Aptamers are experimentally nominated using the well-designed SELEX (systematic evolution of ligands by exponential enrichment) method. Here, we designed a new method for diagnosis and blocking SARS-CoV-2 based on G-quadruplex aptamer. This aptamer was developed against the receptor-binding domain (RBD) region of the spike protein. In the current study, ten quadruplex DNA aptamers entitled AP1, AP2, AP3, AP4, AP5, AP6, AP7, AP8, AP9, and AP10 were designed in silico and had high HADDOCK scores. One quadruplex aptamer sequence (AP1) was selected based on the interaction with RBD of SARS-CoV-2. Results showed that AP1 aptamer could be used as an agent in the diagnosis and therapy of SARS-CoV-2, although more works are still needed. © 2021
Microbial Cell Factories (14752859)20(1)
Background: The objective of this work was to engineer Deinococcus radiodurans R1 as a microbial cell factory for the production of pinene, a monoterpene molecule prominently used for the production of fragrances, pharmaceutical products, and jet engine biofuels. Our objective was to produce pinene from glycerol, an abundant by-product of various industries. Results: To enable pinene production in D. radiodurans, we expressed the pinene synthase from Abies grandis, the geranyl pyrophosphate (GPP) synthase from Escherichia coli, and overexpressed the native 1-deoxy-d-xylulose 5-phosphate synthase. Further, we disrupted the deinoxanthin pathway competing for the substrate GPP by either inactivating the gene dr0862, encoding phytoene synthase, or substituting the native GPP synthase with that of E. coli. These manipulations resulted in a D. radiodurans strain capable of producing 3.2 ± 0.2 mg/L pinene in a minimal medium supplemented with glycerol, with a yield of 0.13 ± 0.04 mg/g glycerol in shake flask cultures. Additionally, our results indicated a higher tolerance of D. radiodurans towards pinene as compared to E. coli. Conclusions: In this study, we successfully engineered the extremophile bacterium D. radiodurans to produce pinene. This is the first study demonstrating the use of D. radiodurans as a cell factory for the production of terpenoid molecules. Besides, its high resistance to pinene makes D. radiodurans a suitable host for further engineering efforts to increase pinene titer as well as a candidate for the production of the other terpenoid molecules. © 2021, The Author(s).
International Journal of Peptide Research and Therapeutics (15733149)27(1)pp. 309-316
The Glutathione S-Transferases (GSTs) are detoxification enzymes which exist in variety of living organisms such as bacteria, fungi, plants and animals. These multifunctional enzymes play important roles in the biosynthesis of steroids, prostaglandins, apoptosis regulation, and stress signaling. In this study, we designed a method to independently predict the structures of animal, fungal and plant GSTs using Chou’s pseudo-amino acid composition concept. Support vector machine (SVM), Random Forests (RF), Covariance Discrimination (CD) and Optimized Evidence-Theoretic K-nearest Neighbor (OET-KNN) were used as powerful machine learnings algorithms. Based on our results, Random Forests demonstrated the best prediction for animal GSTs with 0.9339 accuracy and SVM showed the best results for fungal and plant GSTs with 0.8982 and 0.9655 accuracy, respectively. Our study provided an effective prediction for GSTs based on the concept of PseAAC and four different machine learning algorithms. © 2020, Springer Nature B.V.
International Archives of Allergy and Immunology (14230097)181(11)pp. 813-821
Background: A large number of allergens are derived from plant and animal proteins. A major challenge for researchers is to study the possible allergenic properties of proteins. The aim of this study was in silico analysis and comparison of several physiochemical and structural features of plant- and animal-derived allergen proteins, as well as classifying these proteins based on Chou's pseudo-amino acid composition (PseAAC) concept combined with bioinformatics algorithms. Methods: The physiochemical properties and secondary structure of plant and animal allergens were studied. The classification of the sequences was done using the PseAAC concept incorporated with the deep learning algorithm. Conserved motifs of plant and animal proteins were discovered using the MEME tool. B-cell and T-cell epitopes of the proteins were predicted in conserved motifs. Allergenicity and amino acid composition of epitopes were also analyzed via bioinformatics servers. Results: In comparison of physiochemical features of animal and plant allergens, extinction coefficient was different significantly. Secondary structure prediction showed more random coiled structure in plant allergen proteins compared with animal proteins. Classification of proteins based on PseAAC achieved 88.24% accuracy. The amino acid composition study of predicted B- and T-cell epitopes revealed more aliphatic index in plant-derived epitopes. Conclusions: The results indicated that bioinformatics-based studies could be useful in comparing plant and animal allergens. © 2020 S. Karger AG, Basel. All rights reserved.
Journal of Biotechnology (01681656)308pp. 56-62
Alkaline phosphatase (ALP) and acid phosphatase (ACP) are two important phosphatase enzymes that play fundamental roles in Gram-negative bacteria. Additionally, they are useful for various biotechnological and industrial applications. In the present study, different aspects of bacterial ALPs and ACPs such as pseudo amino acid composition (PseAAC), amino acid composition, dipeptide composition, physicochemical properties, secondary structures and structural motifs were studied. The binding affinity of the phosphomonoesters to ALP and ACP enzymes was predicted by docking, and the activity of ALPs and ACPs were measured using colorimetric assay. ROC curve statistical analysis the machine learning algorithms were applied for classification of these two phosphatase protein groups. The results indicated that the physicochemical properties of ALPs and ACPs were not significantly different, although the aliphatic index and Extinction coefficient of motifs of these two enzymes were significantly different. Classification based on the concept of PseAAC and dipeptide composition also indicated high accuracy. The result of docking demonstrated that the binding free energy of ALPs was less than ACPs and the experimental results demonstrated that the activity of ACPs was more than ALPs. In conclusion, there is a relationship between efficiency and PseAAC and dipeptide compositions of these two enzymes. © 2019 Elsevier B.V.
Molecular Biology Research Communications (2322181X)9(2)pp. 71-82
Human papillomaviruses (HPV) are a group of strong human carcinogen viruses considered to be the fourth leading cause of mortality among women in the world. HPV is the most important cause of cervical cancer, which is the second most common cancer in women living in low and middle-income countries. To date, there is no effective cure for an ongoing HPV infection; therefore, it is required to investigate anticancer drugs against this life-threatening infection. In this study, we collected more than 100 plant-derived compounds with anti-cancer and antiviral potentials from a variety of papers. Smile formats of these compounds (ligand), were harvested from PubChem database and examined based on the absorption, distribution, metabolism, excretion, and toxicity properties by programs such as Swiss ADME, admetSAR, and pkCSM. Twenty compounds, which were likely to be the HPV16E6 inhibitor, were selected for docking calculations. We examined these natural inhibitors against the HPV16 E6 oncogenic protein. Eventually, three of these compounds were used as the most potent inhibitors (Ginkgetin (peculiarly), Hypericin and Apigetrin) were probably used as the possible source of cancer treatment caused by E6 oncoprotein. In this research, we conducted the docking calculations by Autodock 4.2.6 software. Docking analysis showed the interaction of these plant-originated inhibitors with E6AP, p53, and Myc binding sites on the E6 oncoprotein which support the normal function of E6AP, p53, and Myc. © 2020 Shiraz University.
SLAS Discovery (24725552)25(9)pp. 1087-1093
Nucleic acid aptamers that specifically bind to other molecules are mostly obtained through the systematic evolution of ligands by exponential enrichment (SELEX). Because SELEX is a time-consuming procedure, the in silico design of specific aptamers has recently become a progressive approach. HIV-1 surface glycoprotein gp120, which is involved in the early stages of HIV-1 infection, is an attractive target for RNA and DNA aptamer selection. In this study, four single-stranded DNA aptamers, referred to as HD2, HD3, HD4, and HD5, that had the ability of HIV-1 inhibition were designed in silico. In a proposed non-SELEX approach, some parts of the B40 aptamer sequence, which interacted with gp120, were isolated and considered as a separate aptamer sequence. Then, to obtain the best docking scores of the HDOCK server and Hex software, some modifications, insertions, and deletions were applied to each selected sequence. Finally, the cytotoxicity and HIV inhibition of the selected aptamers were evaluated experimentally. Results demonstrated that the selected aptamers could inhibit HIV-1 infection by up to 80%, without any cytotoxicity. Therefore, this new non-SELEX approach could be considered a simple, fast, and efficient method for aptamer selection. © 2020 Society for Laboratory Automation and Screening.
International Immunopharmacology (18781705)78
This study was aimed to introduce a novel algorithm for determining linear B- and T-cell epitopes from Crimean-Congo haemorrhagic fever virus (CCHFV) antigens. To this end, 387 approved B- and T-cell epitopes, as well as 331 non-epitope peptides from different serotypes of the virus were collected from IEDB database for generating of the train datasets. After that, the physicochemical properties of the epitopes were expressed as the numeric vectors using Chou's pseudo amino acid composition method. The vectors then were used for training of four machine learning algorithms including artificial neural network (ANN), k-nearest neighbors (kNN), support vector machine (SVM) and Random forest (RF). The results confirmed that ANN was the most accurate algorithm for discriminating between the epitopes and non-epitopes with the accuracy of 0.90. Furthermore, for evaluating the performance of the ANN algorithm, an epitope prediction challenge was performed to a random peptide library from envelopment polyprotein of CCHFV. Moreover, the efficiency of the predicted epitopes in term of antigenicity and affinity to MHC-II were compared to the predicted epitope by standard epitope prediction tools based on their VaxiJen 2.0 score and molecular docking outputs. Finally, the ability of the screened epitopes to stimulation of humoral and cellular responses was evaluated by an in silico immune simulation process thought C-Immsim 10.1 server. The results confirmed that this method has more accuracy for epitope-mapping than the standard tools and could considered as an effective algorithm to develop a serotype independent one-click automated epitope based vaccine design tool. © 2019 Elsevier B.V.
Applied Biochemistry and Biotechnology (02732289)190(3)pp. 1035-1048
Laccases are a group of enzymes with a critical activity in the degradation process of both phenolic and non-phenolic compounds. These enzymes present in a diverse array of species, including fungi and bacteria. Since this enzyme is in the market for different usages from industry to medicine, having a better knowledge of its structures and properties from diverse sources will be useful to select the most appropriate candidate for different purposes. In the current study, sequence- and structure-based characteristics of these enzymes from fungi and bacteria, including pseudo amino acid composition (PseAAC), physicochemical characteristics, and their secondary structures, are being compared and classified. Autodock 4 software was used for docking analysis between these laccases and some phenolic and non-phenolic compounds. The results indicated that features including molecular weight, aliphatic, extinction coefficient, and random coil percentage of these protein groups present high degrees of diversity in most cases. Categorization of these enzymes by the notion of PseAAC, showed over 96% accuracy. The binding free energy between fungal laccases and their substrates showed to be considerably higher than those of bacterial ones. According to the outcomes of the current study, data mining methods by using different machine learning algorithms, especially neural networks, could provide valuable information for a fair comparison between fungal and bacterial laccases. These results also suggested an association between efficacy and physicochemical features of laccase enzymes from different sources. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.
Journal of Biotechnology (01681656)306pp. 1-8
Carcinoembryonic antigen (CEA), a highly glycosylated protein, overexpresses in many cancers. In this study, computational methods were used to optimize CEA aptamers. Experimental evaluvation of selected aptamers were conducted through electrochemical impedance spectroscopy. After two and three-dimensional structure modeling, the complexes of twelve reported aptamers against CEA were simulated using the ZDOCK server. Based on docking scores, two aptamer sequences (CSR59 and CSR57.1) were selected and used to create a new library. This ssDNA aptamer library consisting of 91 sequences was created using diverse in silico mutational methods. We obtained seventeen sequences having higher binding scores than reported sequences. Based on ZDOCK scores, the interaction domain of CEA, and steric hindrance due to glycosylation, two aptamer sequences (G3S1.5 and G2S2.2) were selected. An impedimetric aptasensor was designed, and selected aptamers were used as biorecognition elements. Resistance to charge transfer (Rct) quantities confirmed the bioinformatic approach and molecular docking scores. The result showed that the interaction ability of selected aptamers was about 13.5 fold higher than the control. It can be concluded that the selected aptamers have good potential for detection of carcinoembryonic antigen biomarker. © 2019
Applied Biochemistry and Biotechnology (02732289)187(1)pp. 90-100
One of the most dangerous human pathogens with high prevalence worldwide is Streptococcus pyogenes, which has major impacts on global morbidity and mortality. A major challenge for S. pyogenes vaccine development is the detection of epitopes that confer protection from infection by multiple S. pyogenes types. Our aim was to identify the most conserved and immunogenic antigens of S. pyogenes, which can be a potential candidate for vaccine design in the future. Eight important surface proteins were analyzed. Using different prediction servers, strongest epitopes were selected. They had the ability to stimulate the humoral and cell-mediated immune system. Molecular docking was performed for measuring free-binding energy of selected epitopes. Seven epitopes from three surface proteins were selected as potential candidates for vaccine development. Conservation of selected epitopes among different Streptococcus types was checked. Further in vitro and in vivo tests are required to validate the suitability of the epitopes for vaccine design. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.
Molecular Biology Research Communications (2322181X)8(2)pp. 91-98
A great number of researches over the last years are allocated to know cancer reasons, prevention and treatment strategies. Bacterial infections are one of the promoting factors in cancer development. The present study was carried out to study effects of heat-killed bacteria on cancer cell lines MCF7 and HT-29. To this purpose, four bacterial strains including Salmonella typhi, Staphylococcus epidermidis, Escherichia coli and Pseudomonas aeruginosa were assayed. Thermal inactivation method was used to kill the bacteria and preserve the bacterial surface proteins unchangeable. The concentrations of 0.01, 0.1, 0.5 and 1 mg/ml of inactivated bacteria were prepared to evaluate the effects of heat-inactivated bacterial solutions on MCF7 and HT-29 cell lines. MTT assay was used to measure the cell viability of cancer cells treated with different concentration of inactivated bacterial solutions.The MTT assay results after 48 hours showed that the heat-killed bacterial solutions were able to induce the proliferation of both cancer cell lines. In addition, the most cell viability in MCF-7 cell line was seen in samples treated with S. epidermidis, while in HT29 cells, the most one was seen in S. typhi treated samples. It was concluded that bacterial infections are cancer-deteriorating agents, and any species of bacteria is specific to certain cancerous tissue. © 2019 Shiraz University.
Journal of Biomedical Informatics (15320480)93
Crimean-Congo hemorrhagic fever (CCHF) is considered one of the major public health concerns with case fatality rates of up to 80%. Currently, there is no effective approved vaccine for CCHF. In this study, we used a computer-aided vaccine design approach to develop the first multi-epitope recombinant vaccine for CCHF. For this purpose, linear B-cell and T-cell binding epitopes from two structural glycoproteins of CCHF virus including Gc and Gn were predicted. The epitopes were further studied regarding their antigenicity, allergenicity, hydrophobicity, stability, toxicity and population coverage. A total number of seven epitopes including five T-cell and two B-cell epitopes were screened for the final vaccine construct. Final vaccine construct composed of 382 amino acid residues which were organized in four domains including linear B-cell, T-cell epitopes and cholera toxin B-subunit (CTxB) along with heat labile enterotoxin IIc B subunit (LT-IIc) as adjuvants. All the segments were joined using appropriate linkers. The physicochemical properties as well as the presence of IFN-γ inducing epitopes in the proposed vaccine, was also checked to determining the vaccine stability, solubility and its ability to induce cell-mediated immune responses. The 3D structure of proposed vaccine was subjected to the prediction of computational B-cell epitopes and molecular docking studies with MHC-I and II molecules. Furthermore, molecular dynamics stimulations were performed to study the vaccine-MHCs complexes stability during stimulation time. The results suggest that our proposed vaccine was stable, well soluble in water and potentially antigenic. Results also demonstrated that the vaccine can induce both humoral and cell-mediated immune responses and could serve as a promising anti-CCHF vaccine candidate. © 2019 Elsevier Inc.
Journal Of Herbmed Pharmacology (23455004)7(3)pp. 176-184
Introduction: Streptococcus mutans is a principal pathogenic agent in biofilm formation on the teeth surfaces and subsequently development of dental caries and plaque. Therefore, currently introducing novel anti-bacterial and anti-biofilm agents, especially plant based materials are highly regarded. This study was planned to investigate in silico and in vitro antibacterial activities of Prangos acaulis extracts against S. mutans in single and biofilm forms and their mutagenicity in Ames test. Methods: The anti-bacterial and anti-biofilm effects of methanol extracts from various parts of P. acaulis were evaluated using disk diffusion and microtiter assay. Moreover, the potential mutagenicity of the extracts was investigated using Ames test. In addition, dominant constitutes of P. acaulis that reported in previous studies were subjected to an in silico analysis. The ability of selected phytochemicals to inhibit the glucosyltransferase was evaluated using molecular docking method. Results: All tested extracts especially root extract had significant antibacterial activity against the single form of S. mutans and inhibited biofilm formation without any mutagenic activity. The results also confirmed that three compounds consisting of ar-curcumene, d-limonene and alpha-pinene had strong and appropriate interactions to glucosyltransferase. Conclusion: This study indicated that P. acaulis has potent antibacterial and biofilm inhibition activity against S. mutans and can be good candidate for in vitro and in vivo studies with the aim of introducing novel inhibitors of dental caries development. © 2018, Nickan Research Institute.
Journal of Bioinformatics and Computational Biology (02197200)16(4)
With the increase in immunocompromised patients in the recent years, fungal infections have emerged as new and serious threat in hospitals. This, and the insufficiency of current antifungal therapies alongside their toxic effects on patients, has led to the increased interest in seeking new antifungal peptides. In the present study, we have developed a prediction method for screening of antifungal peptides. For this, we have chosen Chou's pseudo amino acid composition (PseAAC) to translate peptide sequences into numeric values. Thus, the SVM classifier was performed for binomial classification of antifungal peptides. The performance of the classifier was evaluated via ten-fold cross-validation and an independent dataset. For further validation of the model developed, 22 P24-derived peptides were predicted using the classifier and in vitro assays were performed on the three peptides with the highest prediction score. The results showed that the PseAAC + SVM method is able to predict AFPs with ACC of 94.76%. In vitro results also validate the SEN and SPC of the classifier. The results suggest that the computational approach used in this study is highly efficient for prediction of antifungal peptides, which can save time and money in AFP screening and synthesis of novel peptides. © 2018 World Scientific Publishing Europe Ltd.
Iranian Journal of Science and Technology, Transaction A: Science (10286276)42(4)pp. 1805-1811
Reverse transcriptase (RT) is an important enzyme for retrovirus replication in susceptible target cells. RT of HIV-1 is one of the key targets for anti-HIV drugs. In contrast, HIV-2 RT reveals a basic resistance to non-nucleoside RT inhibitors (NNRTIs). In the present study, a comparison of different aspects of RT proteins in HIV-1 and HIV-2 such as pseudo amino acid composition (PseAAC), conventional amino acid composition (AAC), physicochemical properties, secondary structures and structural motifs has been performed. Statistical analysis and support vector machine (SVM) algorithm have been used for final comparison of two RT protein groups. The results demonstrate that AAC of four amino acids (Ala, Leu, Gln and Ser), molecular weight and percentage of alpha helix of RT proteins are significantly different between these two types. Classification based on the concept of PseAAC also showed 100% accuracy and highlighted that pseudo pI and pseudo pKa values are significant differences between two RT groups. In conclusion, the results indicate that the computational techniques can provide useful information for comparing HIV-1 and HIV-2 RTs. Our results may also explain the dissimilarity between the susceptibility of HIV-1 and HIV-2 to different drugs. © 2017, Shiraz University.
Journal of Molecular Liquids (18733166)265pp. 243-250
HIV-1 P24 protein-derived peptides-loaded chitosan nanoparticles (CS-NPs) were synthesized, based on the ionic gelation method and development of electrostatic interactions between CS-NPs and negatively charged of HIV-1 P24 protein-derived peptides. Dynamic light scattering analysis (DLS) revealed that CS-NPs had a mean diameter of 22 nm. The prepared peptides loaded CS-NPs showed that peptide loading via incubation method led to an increase in the particle size to 70 nm, in comparison to CS-NPs. The results obtained by Zetasizer revealed that the surface charge of CS-NPs is positive due to the presence of amine groups on its surface. Peptide adsorption on the nanoparticles would have decreased the positive surface charge of the cationic chitosan molecule and led to the decline in the values of zeta-potential in CS-NPs from+30.3 to+23.2 mV. The rate of loading efficiency became 96%, the peptide was very quickly released in the first 24 h, and after that the releasing rate was decreased. After 216 h, >70% of the drug was released. Since the use of peptides in high concentrations is not economically feasible, this paper attempts to use the nano-carrier to overcome this limitation. The novelty of this work is to use of chitosan nanoparticles to increasing the effectiveness of peptides at low concentrations. © 2018 Elsevier B.V.
Behbahani, M.,
Nosrati, M.,
Mohabatkar, H.,
Behbahani, M.,
Nosrati, M.,
Mohabatkar, H. Applied Biochemistry and Biotechnology (2732289)185(3)pp. 786-798
Lysozyme is a relatively small enzyme with different biological activities, which is found in tears, saliva, egg white, and human milk. In the study, the anti-HIV-1 activity of lysozymes purified from quail, Meleagris, and hen egg white has been determined. For this end, a time-of-drug-addition assay was performed to identify the target of anti-HIV-1 agents and for determination of probable anti HIV-1 mechanism of the studied lysozyme, the binding affinity of the lysozymes to the human CD4 receptor was studied by molecular docking method. To define structural differences between studied lysozymes, structural motifs of them were predicted by MEME tool. Quail, hen, and Meleagris lysozymes showed potent anti-HIV-1 activity with EC50 of 7.5, 10, and 55 nM, respectively. The time-of-drug-addition study demonstrated that the inhibitory effect of all purified lysozymes is before HIV-1 infection. The frequency and intensity of CD4 expression in PBMCs decreased in the presence of all mentioned lysozymes. Also, the expression level of C-C chemokine receptor type 5 (CCR5) and chemokine receptor type 4 (CXCR4) on CD4+ T cells was not changed in cells treated with these lysozymes. The results of in silico study confirmed that the binding energy of quail lysozyme with CD4 was more than that of other studied lysozymes. The results revealed that these lysozymes restrict HIV-1 attachment to host cell CD4. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.
Meta Gene (22145400)17pp. 23-27
The purpose of the work was to study mutation screening of BRCA1 in Iranian patients with sporadic breast cancer. We carried out a mutational analysis of BRCA1 gene in 101 breast cancer patients from a population in Central of Iran. The comparison of DNA of paraffin-embedded breast cancer tissue from patients was studied, and breast tissue from 30 unrelated normal women without cancer was selected as controls. The entire BRCA1 coding sequence was amplified by PCR with primers especially designed for comprehensive mutation screening by single-strand conformation polymorphism (SSCP) analysis. The PCR products revealing abnormal SSCP migration pattern were sequenced. Then, in silico investigation was performed to identify the effects of new mutations on stability and function of BRCA 1.A total of ten nucleotide alterations were observed in the breast cancer tissue DNA. Six cases of single nucleotide changes in BRCA1 were detected in the study without records in the BIC database consisted four polymorphism in exon 11 (1543 Del G, 1597C>T, 2246 Del T, 2612C>G), one missense mutation in exon 7 (490C>T), and one deletion mutation in exon 10 (743 Del C). No nucleotide alterations were detected in the controls. In addition, the results of in silico analysis indicated that three mutations including 2612C>G, 1543 Del G and 743 Del C were not recorded in the especial database. Furthermore, the results of molecular docking studies confirmed that 2612C>G could change physicochemical properties of BRCA1.The findings of the present study suggest that screened mutations may have an important role on the incidence of breast cancer in women. © 2018 Elsevier B.V.
Molecular Biology Research Communications (2322181X)7(1)pp. 35-41
Streptococcal bacteria are among dangerous human pathogens with major prevalence worldwide. A good vaccine against streptococcal bacteria should have epitopes that confer protection from infection by different streptococcal bacteria types. we aimed was to recognize the most immunogenic and conserved epitopes of streptococcal bacteria, which could be a potential candidate for vaccine development. Nineteen different M proteins of different streptococcal bacteria were chosen and analyzed. Nine-mer epitopes able to simulate both cells mediate and humoral immunity were predicted. Molecular docking was applied in order to measure free binding energy of selected epitopes. Final epitopes were analyzed if they were conserved among different streptococcal bacteria. The identified epitopes require experimental validation for their potential use in peptide vaccines. © 2018, Shiraz University.
Molecular Biology Research Communications (2322181X)6(2)pp. 57-64
The present investigation was carried out to evaluate anticancer activity of cow, goat, sheep, mare, donkey and camel milks and their casein and whey proteins against MCF7 cell line. The structure-based properties of the casein proteins were also investigated, using bioinformatics tools to find explanation for their antitumor activities. The effect of different milks and their casein and whey proteins on MCF7 proliferation was measured using MTT assay at different concentrations (0.5, 1 and 2 mg/ml). The results showed that mare, donkey, cow and camel milks and their casein and whey proteins have potent cytotoxic activity against MCF7 cells in a dose dependent manner while sheep and goat milks and their proteins did not reveal any cytotoxic activity. The in silico results demonstrated that mare, donkey and camel caseins had highest positive and negative charges. The secondary structure prediction indicated that mare and donkey caseins had the maximum percentage of α helix and camel casein had the highest percentage of extended strand. This study suggests that there is a striking correlation between anti-cancer activity of milk caseins and their physicochemical properties such as alpha helix structure and positive and negative charges. In conclusion, the results indicated that mare, camel and donkey milks might be good candidates against breast cancer cells.
Current Topics In Medicinal Chemistry (15680266)17(21)pp. 2381-2392
Post translational modification (PTM) is one of the critical levels in regulation of gene expression that determines the fate of proteins after translation in eukaryotic cells. Since the detection of PTM sites in proteins is useful for diagnosis and prevention of diseases, numerous web-tool predictors are introduced to predict various types of PTMs. In this paper, an attempt is made to summarize a number of server predictors for the prediction of PTM sites. © 2017 Bentham Science Publishers.
Medicinal Chemistry (15734064)12(8)pp. 795-800
Background: Fungi are an emerging threat in medicine and agriculture and current therapeutics have proved to be insufficient and toxic. This has led to an increased interest in peptide-based therapeutics, especially antifungal peptides (AFPs), being safer and more effective drug candidates against fungal threats. However, screening for peptides with antifungal activity is costly and timeconsuming. However, by using computational techniques, we can overcome these restricting factors. The aim of the present study is to compare different machine learning algorithms in combination with Chou's pseudo amino acid composition in classifying and predicting AFPs to represent a precise model for AFP prediction. Methods: Five different machine learning algorithms frequently used for classification of biological data were used and their performance was evaluated and compared based on their accuracy, sensitivity, specificity and Matthew's correlation coefficient. The two algorithms with the best performance were then further verified with an independent test dataset. Results: SVM and Bagged-C4.5 classifiers had the highest performance results among the five algorithms. Further validations showed that the model generated using SVM can be employed for precise classification and prediction of antifungal peptides. All the performance values of this model were above 80%, making the classifier highly accurate and trustable. Conclusion: Using computational approaches, especially data mining techniques, we can develop a precise prediction model for antifungal peptides. The model developed in this study using SVM can be considered a powerful tool for the prediction of antifungal peptides, which can be the first step in synthesis and discovery of novel fungi targeting agents. © 2016 Bentham Science Publishers.
Journal of Theoretical Biology (10958541)411pp. 1-5
Lignin peroxidases (LiPs) are important enzymes in the degradation process of lignin which are presented in different species of fungi and bacteria. In the present study, sequence and structure-based properties of LPs in fungi and bacteria are compared. These properties include pseudo amino acid composition (PseAAC), physicochemical properties and the secondary structure. Autodock 4 has been used for docking between LiPs and lignan. The motifs of LiP were predicted by MEME tool. Statistical analysis and Multinomial Naïve Bayes (MNB) algorithm were used for the classification of two LiP protein groups. The results demonstrated that molecular weight, isoelectric point, aliphatic, extinction coefficient and random coil percentage of LiPs in fungi and bacteria were significantly different between these two groups. The classification of these two groups based on the concept of PseAAC showed over 80% accuracy. The binding free energy between bacterial LiPs and lignan is significantly more than fungi LiP and ligand. The aliphatic and instability of most important motifs of bacteria and fungi were significantly different. In conclusion, the results indicated that computational techniques could provide useful information for comparing fungal and bacterial LiPs. These results can also explain that there is a relationship between efficacy and physicochemical properties of LiPs. © 2016 Elsevier Ltd
Journal of Mazandaran University of Medical Sciences (17359260)26(142)pp. 82-95
Background and purpose: Currently medicinal plants as immunomodulator or antimicrobial agents have gained interests in pharmaceutical researches. The aim of this study was to evaluate antibacterial activity, mutagenicity and proliferator effect of different parts of seven species of Artemisia genus on human lymphocyte cells of methanolic extracts. Materials and methods: In this experimental study the plant materials were collected, identified, air dried, and powdered. Then, the plant materials were extracted by methanol using maceration method. Antibacterial activity was determined by disk diffusion method. Also, mutagenic and proliferative activities of the extracts were evaluated by Ames test and MTT assay, respectively. Results: None of the species showed mutagenic activity. The extracts from the flowers and roots in all tested species showed high antibacterial and proliferative activities. Artimisia vulgaris and A. sieberi had the most and least antibacterial activity, respectively. On the other hand, A. khorasanica and A. deserti showed the highest and lowest proliferative effects on human lymphocyte cells, respectively. Conclusion: In this investigation none of the species showed mutagenic activity. We also observed significant antibacterial and proliferative activities in flower and root extracts. © 2016, Mazandaran University of Medical Sciences. All rights reserved.
Iranian Journal of Science and Technology, Transaction A: Science (10286276)40(4)pp. 275-279
Probiotics are beneficial bacteria that exert beneficial health effects on the host. These bacteria produce lactic acid as a product of fermentation. The aim of this study was to optimize growth and production of lactic acid by three strains of probiotic bacteria at different concentrations of sucrose, glucose, stevia leaf and stevioside. These three strains were Lactobacillus casei, Lactobacillus brevis and Lactobacillus plantarum. Lactic acid production and bacterial growth were, respectively, estimated by use of gas chromatography and colony-forming units (CFU) assay. The highest bacterial growth and lactic acid production in these three strains were obtained by high concentration of sucrose. Among these three bacteria, Lact. casei and Lact. brevis can produce more lactic acid compared to Lact. plantarum. All strains could produce lactic acid in the presence of sucrose, glucose and stevia leaf extract in a dose dependent manner. The effect of stevioside on lactic acid production in these strains at high and low concentrations was almost same. In conclusion, data indicate that sucrose is the best carbon source for lactic acid production and bacterial growth. Stevioside and stevia leaf also have a good potential to increase lactic acid production in these three strains. © Shiraz University 2016.
International Journal of Peptide Research and Therapeutics (15733149)21(1)pp. 57-62
Human immunodeficiency virus-1 (HIV-1) is the etiological agent for the global concerning disease "AIDS". The virus infects 35 million people globally and after 30 years, the disease remains a challenge. Despite great efforts in finding efficient treatment strategies, the pandemic of AIDS is continuing and the rate of new infections has not been diminished. Therefore, the need for finding novel treatment strategies is still of great importance. Peptide-based therapeutics has shown promise in the treatment of many challenging diseases such as various types of cancers and also HIV. Since time and money are the two restricting factors in any experimental researches, computer-aided techniques can dramatically reduce time and costs. In the present study, we developed a method based on pseudo amino acid composition of amino acid sequences to classify the anti-HIV-1 peptides using different machine learning algorithms. The performance of each algorithm was investigated and after comparing the performance parameters, the most accurate algorithm was proposed for predicting anti-HIV-1 activity of any given peptide. Having the accuracies of 96.15 and 83.71 % respectively, multilayer perceptron (MLP) and logistic model tree algorithms were primarily shown to be the most accurate ones in classifying anti-HIV-1 peptides. Final results demonstrate that model generated by MLP can be a valuable tool for the classification and prediction of anti- HIV-1 peptides in order to have a preliminary prediction which can be further coupled with experimental assays while reducing time and costs. © Springer Science+Business Media 2014.
Current Nutrition And Food Science (22123881)11(1)pp. 16-20
The present study investigated the mutagenicity of fruit and leaf extracts of five Iranian grape cultivars and their effect on human peripheral blood mononuclear cells (PBMC) proliferation. The grape cultivars studied were: Bidane sefid, Shahroodi, Halvaie, Yaghoti and Ghermez yaghoti dorosht. The effect of the methanol extracts of Vitis vinifera cultivars on PBMC proliferation were measured using MTT assay at different concentrations (100, 1000, 2000, 3000 µg/ml). The mutagenicity of these extracts at two concentrations (1000, 3000 µg/ml) was also investigated on Salmonella typhimurium strain TA98. Among these five species, methanol old leaf and seed extracts strongly increased PBMC proliferation. The grape juices of all cultivars did not have any effect on PBMC proliferation. The grape juices of all species were also found to have potent mutagenicity on S. typhimurium. But skin, seed and leaf extract of all cultivars didn’t show any mutagenicity on this strain. This study provides data concerning the Immune-enhancing activity of fruit, leaf extracts of grape as well as weak mutagenic potency of grape juice. © 2015 Bentham Science Publishers
Journal Of Arthropod-Borne Diseases (23222271)9(1)pp. 116-124
Background: The aim of this study was to generate in silico 3D-structure of the envelope protein of AHFV using homology modeling method to further predict its conformational epitopes and help other studies to investigate its structural features using the model. Methods: A 3D-structure prediction was developed for the envelope protein of Alkhumra haemorrhagic fever virus (AHFV), an emerging tick-borne flavivirus, based on a homology modeling method using M4T and Modweb servers, as the 3D-structure of the protein is not available yet. Modeled proteins were validated using Modfold 4 server and their accuracies were calculated based on their RSMDs. Having the 3D predicted model with high quality, conformational epitopes were predicted using DiscoTope 2.0. Results: Model generated by M4T was more acceptable than the Modweb-generated model. The global score and Pvalue calculated by Modfold 4 ensured that a certifiable model was generated by M4T, since its global score was almost near 1 which is the score for a high resolution X-ray crystallography structure. Furthermore, itsthe P-value was much lower than 0.001 which means that the model is completely acceptable. Having 0.46 Å rmsd, this model was shown to be highly accurate. Results from DiscoTope 2.0 showed 26 residues as epitopes, forming conformational epitopes of the modeled protein. Conclusion: The predicted model and epitopes for envelope protein of AHFV can be used in several therapeutic and diagnostic approaches including peptide vaccine development, structure based drug design or diagnostic kit development in order to facilitate the time consuming experimental epitope mapping process.
Monoclonal Antibodies in Immunodiagnosis and Immunotherapy (21679436)34(3)pp. 213-221
Breast cancer is a major public health problem worldwide. Although in Iran cancer is the third cause of death after coronary heart disease and accidents, mortality from cancer has been on the rise during recent decades. About 15% to 20% of patients with invasive breast cancer have abnormally high levels of HER2 protein. HER2 is a specialized protein found on breast cancer cells that controls cancer growth and spread. This study describes the generation and characterization of new anti-HER2 MAbs towards HER2 protein using a chimeric peptide immunogen containing discontinuous B-cell epitope peptide (peptide 626) and promiscuous T-helper epitope (MVF). The specificity of these MAbs was confirmed in various immunoassays, including ELISA, Western blotting, and immunofluorescence. Moreover, the MTT assay results indicated that 5H5 and 5H11 MAbs could reduce the growth of SKBR3 cells by approximately 50% (p<0.05). These MAbs that can reduce cancer cell proliferation would be useful for cancer therapy. Furthermore, the synthetic peptide used in the current work was able to induce the immune system to generate antibodies, especially IgG isotype. Therefore, it could be further used as a peptide cancer vaccine that targets different epitopes or structural domains of HER2 ECD. © Copyright 2015, Mary Ann Liebert, Inc. 2015.
Current Computer-Aided Drug Design (18756697)10(4)pp. 349-353
Acquired immunodeficiency syndrome (AIDS) is one of the most devastating diseases of current century which is caused by the human immunodeficiency virus (HIV). Although great efforts have been done to fight the virus, the need of new therapeutics candidates of any kind still remains. This process needs huge time and experimental endeavor. However, Computer-aided techniques and can speed up the procedure. Currently, cheminformatics tools have proven to be extremely valuable in pharmaceutical research. In the past few decades, a huge number of different molecular descriptors were designed to describe chemical molecules in a quantitative way to make it easy to use them for computational studies. Herein, we present a computational study of anti-HIV small molecules test by the National Cancer Institute (NCI) to introduce the most efficient molecular descriptors for anti-HIV activity. In this regard a dataset of 199 highly active anti-HIV and 174 inactive compounds were defined by 905 molecular descriptors. Data were classified using Random Forest algorithm and the most important molecular descriptors were introduced as the parameters responsible for representing anti-HIV activity. Applying the mentioned computational and cheminformatics methods, it is possible to predict the anti-HIV activity of any given small molecule with high accuracy. © 2014 Bentham Science Publishers.
Genetics in the Third Millennium (24237159)11(4)pp. 3288-3295
Probiotics are useful bacteria that exert beneficial health effects on the host. These bacteria produce lactic acid as the main product of sugar fermentation via lactate dehydrogenase activity. Lactic acid is considered an important chemical compound which has significant applications in pharmaceutical and food industry. In the present study, lactic acid production and in silico properties of lactate dehydrogenase in three strains of probiotic bacteria were investigated. These three strains were Lactobacillus casei, Lactobacillus brevis and Lactobacillus plantarum. These strains were grown in the de Man, Rogose Sharpe (MRS) medium containing different concentrations of sucrose (20, 10, 5, 2.5, 0 g/l). These bacteria were incubated at 37°C for 72 hours. The bacterial growth and lactic acid production were estimated by colony-forming unit (CFU) and Gas Chromatography (GC) analyzes, respectively. In silico properties of lactate dehydrogenase, which is responsible for lactic acid production, was also evaluated. The result showed that 10 and 20% sucrose could greatly induce growth and production of lactic acid in these three strains. Among these three bacteria, L. plantarum and L. casei could produce more lactic acid. The in silico results of lactate dehydrogenase demonstrated that alpha-helix and beta-sheet percentage in L. plantarum and L. casei were significantly more than L. bervis. These results verified that lactate dehydrogenase of L. plantarum and L. casei is a good candidate for genetic engineering processes. © 2014, Iranian Neurogenetics Society. All rights reserved.
Turkish Journal Of Biology (13000152)38(5)pp. 628-632
A novel SARS-like illness called Middle East respiratory syndrome coronavirus (MERS-CoV), caused by an emerging coronavirus, has been a recent cause for concern due to its fatality and pandemic potential. Developing a peptide-based vaccine could be helpful in fighting against the virus. Since the experimental procedure is time-consuming and expensive, computational analysis can play an important role in accelerating the process. Therefore, the aim of this study was to computationally identify cytotoxic T-lymphocyte epitopes presented by the human leukocyte antigen (HLA)-A*0201, as this is the most frequent HLA class I allele among Middle Eastern populations. The receptor-binding domain of the spike glycoprotein of MERS-CoV, by which the virus binds to its entry receptor to further infect host cells, is a potential candidate used here for running our in silico epitope identification process. The results include predicted epitopes together with their interaction properties with major histocompatibility complex (MHC) molecules and also the binding behavior of MHC-epitope complexes to human T-cell receptor. Predicted epitopes with the most preferable binding properties are beneficial for vaccine development. Therefore, the huge experimental workload for epitope-based vaccine design will be minimized. © TÜBİTAK.
Tumor Biology (14230380)35(12)pp. 12049-12057
Because of direct stimulating immune system against disease, vaccination or active immunotherapy is preferable compared to passive immunotherapy. For this purpose, a newly designed chimeric peptide containing epitopes for both B and T cells from HER2 ECD subdomain III was proposed. To evaluate the effects of the active immunization, a discontinuous B cell epitope peptide was selected based on average antigenicity by bioinformatics analysis. The selected peptide was collinearly synthesized as a chimera with a T helper epitope from the protein sequence of measles virus fusion (208-302) using the GPSL linker. Three mice were immunized with the chimeric peptide. Reactive antibodies with HER2 protein in ELISA and immunofluorescence assays with no cross-reactivity were generated. The 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay indicated that the anti-peptide sera had inhibitory effects on proliferation of SK-BR-3 cells. Hence, the newly designed, discontinuous chimeric peptide representing B and T cell epitopes from subdomain III of HER2-ECD can form the basis for future vaccines design, where these data can be applied for monoclonal antibody production targeting the distinct epitope of HER2 receptor compared to the two broadly used anti-HER2 monoclonal antibodies, Herceptin and pertuzumab. © 2014, International Society of Oncology and BioMarkers (ISOBM).
Applied Biochemistry and Biotechnology (02732289)172(1)pp. 188-195
Human papillomavirus (HPV) is an important pathogen which is classified into two, high- and low-risk groups. The proteins of high-risk and low-risk HPV types have different functions. Therefore, there is a need to develop a computational method for predicting these two groups. In the present study, the physiochemical properties of all early (E1, E2, E4, E5, E6, and E7) and late (L1 and L2) proteins in high- and low-risk HPV types have been studied. The concept of receiver operating characteristic analysis and support vector machines methods has been used for comparison of high- and low-risk HPV types. The results demonstrate that amino acid composition, physiochemical, and secondary structure of E2 protein are significantly different between these two groups. The results demonstrate that in silico properties can create useful information to predict high-risk and low-risk HPV types. © 2013 Springer Science+Business Media New York.
Journal of Theoretical Biology (10958541)341pp. 34-40
Cancer is an important reason of death worldwide. Traditional cytotoxic therapies, such as radiation and chemotherapy, are expensive and cause severe side effects. Currently, design of anticancer peptides is a more effective way for cancer treatment. So there is a need to develop a computational method for predicting the anticancer peptides. In the present study, two methods have been developed to predict these peptides using support vector machine (SVM) as a powerful machine learning algorithm. Classifiers have been applied based on the concept of Chou's pseudo-amino acid composition (PseAAC) and local alignment kernel. Since a number of HIV-1 proteins have cytotoxic effect, therefore we predicted the anticancer effect of HIV-1 p24 protein with these methods. After the prediction, mutagenicity of 2 anticancer peptides and 2 non-anticancer peptides was investigated by Ames test. Our results show that, the accuracy and the specificity of local alignment kernel based method are 89.7% and 92.68%, respectively. The accuracy and specificity of PseAAC-based method are 83.82% and 85.36%, respectively. By computational analysis, out of 22 peptides of p24 protein, 4 peptides are anticancer and 18 are non-anticancer. In the Ames test results, it is clear that anticancer peptides (ARP788.8 and ARP788.21) are not mutagenic. Therefore the results demonstrate that the described computation methods are useful to identify potential anticancer peptides, which are worthy of further experimental validation and 2 peptides (ARP788.8 and ARP788.21) of HIV-1 p24 protein can be used as new anticancer candidates without mutagenicity. © 2013 Elsevier Ltd.
Open Bioinformatics Journal (18750362)9(1)pp. 13-19
Traditional antiviral therapies are expensive, limitedly available, and cause several side effects. Currently, designing antiviral peptides is very important, because these peptides interfere with the key stage of virus life cycle. Most of the antiviral peptides are derived from viral proteins for example peptide derived from HIV-1 capsid protein. Because of the importance of these peptides, in this study the concept of pseudo-amino acid composition (PseAAC) and machine learning methods are used to classify or identify antiviral peptides. © Zare et al.; Licensee Bentham Open.
Journal of Antivirals and Antiretrovirals (discontinued) (19485964)5(3)pp. 57-61
Objectives: The present investigation was carried out to test anti-HIV-1 activity of pure compounds isolated from aerial part extracts of Ocimum basilicum and its parasite Cuscuta campestris. Materials: The anti-HIV-1 activity of these extracts was performed by use of real-time polymerase chain reaction (PCR) assay and high pure viral nucleic acid kit. Results: The most active fractions were detected by NMR as eugenol and eugenol epoxide respectively in Ocimum basilicum and Cuscuta campestris. The apparent effective concentrations for 50% plaque reduction (EC50) of eugenol and eugenol epoxide were 350 and 80 μg/ml. Time of addition studies demonstrated that the inhibitory effect of eugenol and eugenol epoxide is higher respectively in pre HIV-1 infection and during infection. Conclusion: These results demonstrate that eugenol and eugenol epoxide may prevent HIV-1 replication with two different mechanisms. © 2013 Behbahani M, et al.
Antiviral Research (01663542)97(3)pp. 376-380
Aim: This study was carried out to check antiherpetic substances of crude methanol leaf extract of Avicenna marina and its column chromatographic fractions. Background: Herpes simplex virus 2 (HSV-2) is a harmful pathogen especially in highly susceptible individuals. Materials and methods: The antiherpetic activity of crude methanol extract and sub-fractions was performed in different concentrations (20, 2, 0.2, and 0.02. μg/ml) by use of plaque-forming unit (PFU) assay and real time polymerase chain reaction (PCR) assay. Results: The most active fraction analyzed by NMR contained luteolin 7-O-methylether 3'-O-beta-d-glucoside (LMEG). The other active fraction was detected by HPLC as luteolin. The apparent effective concentrations for 50% plaque reduction (EC50) of crude methanol extract, LMEG, luteolin and ACV were 10, 5, 16.6 and 2.97. μg/ml, respectively. The three extracts showed no cytotoxic effect on Vero cell line at concentrations of 32. μg/ml or below. According to the consequences of time-of-addition studies, antiherpetic compound LMEG exerted an inhibitory effect on the early stage of HSV-2 infection during which it was added. Conclusions: In conclusion, LMEG isolated from A. marina could probably inhibit HSV attachment to the cell membrane and its entry into the cell. © 2013 Elsevier B.V.
Abdolahi, K.,
Mohsenzadeh, S.,
Mohabatkar, H.,
Faghih z., ,
Khalafi-nezhad, A. Iranian Journal of Science and Technology, Transaction A: Science (10286276)37(A1)pp. 93-97
The present study aimed to evaluate the antimicrobial activity of a hetroalkyl oximec synthetic compound derivative (Benzophenone O-4-bromoethyl oxime) against two gram positive and three gram negative bacteria. The antibacterial characteristic of this compound was shown using the circular zone diameter of bacterial growth inhibition by disk-diffusion method. In addition, the random amplified polymorphic DNA (RAPD) technique using twenty-three primers was performed to investigate the DNA polymorphism of bacteria that were affected by the synthetic chemical drug. Among these, only 18 primers were found efficient for reproducible banding pattern. Disappearance or appearance of bands between controls and treatments confirm rearrangements and DNA damages in the priming binding sites of bacterial genome. The results show that the RAPD method can be a useful identification tool for studying the DNA polymorphism created by synthetic chemical drugs. The results obtained with this technique showed significant differences between the RAPD profiles.
Protein And Peptide Letters (09298665)20(2)pp. 180-186
Microbial resistance to antibiotics is a rising concern among health care professionals, driving them to search for alternative therapies. In the past few years, antimicrobial peptides (AMPs) have attracted a lot of attention as a substitute for conventional antibiotics. Antimicrobial peptides have a broad spectrum of activity and can act as antibacterial, antifungal, antiviral and sometimes even as anticancer drugs. The antibacterial peptides have little sequence homology, despite common properties. Since there is a need to develop a computational method for predicting the antibacterial peptides, in the present study, we have applied the concept of Chou's pseudo-amino acid composition (PseAAC) and machine learning methods for their classification. Our results demonstrate that using the concept of PseAAC and applying Support Vector Machine (SVM) can provide useful information to predict antibacterial peptides. © 2013 Bentham Science Publishers.
Medicinal Chemistry (15734064)9(1)pp. 133-137
Because of the importance of proteins in inducing allergenic reactions, the ability of predicting their potential allergenicity has become an important issue. Bioinformatics presents valuable tools for analyzing allergens and these complementary approaches can help traditional techniques to study allergens. This work proposes a computational method for predicting the allergenic proteins. The prediction was performed using pseudo-amino acid composition (PseAAC) and Support Vector Machines (SVMs). The predictor efficiency was evaluated by fivefold cross-validation. The overall prediction accuracies and Matthew's correlation coefficient (MCC) obtained by this method were 91.19% and 0.82, respectively. Furthermore, the minimum Redundancy and Maximum Relevance (mRMR) feature selection method was utilized for measuring the effect and power of each feature. Interestingly, in our study all six characters (hydrophobicity, hydrophilicity, side chain mass, pK1, pK2 and pI) are present among the 10 higher ranked features obtained from the mRMR feature selection method. © 2013 Bentham Science Publishers.
Asian Pacific Journal of Cancer Prevention (15137368)13(7)pp. 3053-3059
Human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor receptor family of receptor tyrosine kinases that plays important roles in all processes of cell development. Their overexpression is related to many cancers, including examples in the breast, ovaries and stomach. Anticancer therapies targeting the HER2 receptor have shown promise, and monoclonal antibodies against subdomains II and IV of the HER2 extra-cellular domain (ECD), Pertuzumab and Herceptin, are currently used in treatments for some types of breast cancers. Since anti HER2 antibodies targeting distinct epitopes have different biological effects on cancer cells; in this research linear and conformational B cell epitopes of HER2 ECD, subdomain III, were identified by bioinformatics analyses using a combination of linear B cell epitope prediction web servers such as ABCpred, BCPREDs, Bepired, Bcepred and Elliprro. Then, Discotope, CBtope and SUPERFICIAL software tools were employed for conformational B cell epitope prediction. In contrast to previously reported epitopes of HER2 ECD we predicted conformational B cell epitopes P1C: 378-393 (PESFDGDPASNTAPLQ) and P2C: 500-510 (PEDECVGEGLA) by the integrated strategy and P4: PESFDGD-X-TAPLQ; P5: PESFDGDP X TAPLQ; P6: ESFDGDP X NTAPLQP; P7: PESFDGDP-X-NTAPLQ; P8: ESFDG-XX-TAPLQPEQL and P9: ESFDGDP-X-NTAPLQP by SUPERFICIAL software. These epitopes could be further used as peptide antigens to actively immune mice for development of new monoclonal antibodies and peptide cancer vaccines that target different epitopes or structural domains of HER2 ECD.
Current Protein And Peptide Science (13892037)13(6)pp. 547-559
Scientists have united in a common search to sequence, store and analyze genes and proteins. In this regard, rapidly evolving bioinformatics methods are providing valuable information on these newly-discovered molecules. Understanding what has been done and what we can do in silico is essential in designing new experiments. The unbalanced situation between sequence-known proteins and attribute-known proteins, has called for developing computational methods or high-throughput automated tools for fast and reliably predicting or identifying various characteristics of uncharacterized proteins. Taking into consideration the role of viruses in causing diseases and their use in biotechnology, the present review describes the application of protein bioinformatics in virology. Therefore, a number of important features of viral proteins like epitope prediction, protein docking, subcellular localization, viral protease cleavage sites and computer based comparison of their aspects have been discussed. This paper also describes several tools, principally developed for viral bioinformatics. Prediction of viral protein features and learning the advances in this field can help basic understanding of the relationship between a virus and its host. © 2012 Bentham Science Publishers.
Protein And Peptide Letters (09298665)18(6)pp. 559-567
The aim of this study was prediction of epitopes and medically important structural properties of protein E of Alkhurma hemorrhagic fever virus (AHFV) and comparing these features with two closely relates viruses, i.e. Kyasanur Forest disease virus (KFDV) and Tick-borne encephalitis virus (TBEV) by bioinformatics tools. Prediction of evolutionary distance, localization, sequence of signal peptides, C, N O glycosylation sites, transmembrane helices (TMHs), cysteine bond positions and B cell and T cell epitopes of E proteins were performed. 2D-MH, Virus-PLoc, Signal-CF, EnsembleGly, MemBrain, DiANNA, BCPREDS and MHCPred servers were applied for the prediction. According to the results, the evolutionary distance of E protein of AHFV and two other viruses was almost equal. In all three proteins of study, residues 1-35 were predicted as signal sequences and one asparagine was predicted to be glycosylated. Results of prediction of transmembrane helices showed one TMH at position 444-467 and the other one at position 476-490. Twelve cysteines were potentially involved to form six disulfide bridges in the proteins. Four parts were predicted as B cell epitopes in E protein of AHFV. One epitope was conserved between three proteins of study. The only conserved major histocompatibility complex (MHC) binding epitope between three viruses was for DRB0401 allele. As there are not much experimental data available about AHFV, computer-aided study and comparison of E protein of this virus with two closely related flaviviruses can help in better understanding of medical properties of the virus. © 2011 Bentham Science Publishers Ltd.
Iranian Journal of Science and Technology, Transaction A: Science (10286276)35(1)pp. 57-60
The impacts of salicylic acid and silicon on some physiological parameters of maize seedlings in the presence of cadmium (100 μM) were investigated. Inhibitory effects of cadmium on seedling growth resulted in reduced shoot and root fresh weight, low percentage of relative water content, low chlorophyll, free proline and soluble sugars contents and a low rate of lipid peroxidation. Results indicated that salicylic acid and silicon alleviate the inhibitory effects of cadmium on maize seedlings by increasing both their chlorophyll content and fresh weight. Although individual treatments of salicylic acid and silicon reduced plants free proline, soluble sugars and cadmium uptake and lipid peroxidation rate, they improved root and shoot fresh weights in both cadmium stressed and unstressed seedlings. When combined, salicylic acid and silicon alleviated the inhibitory effects of cadmium on seedlings significantly.
Mohsenzadeh, S.,
Esmaeili, M.,
Moosavi, F.,
Shahrtash, M.,
Saffari, B.,
Mohabatkar, H. African Journal of Biotechnology (16845315)10(42)pp. 8160-8165
Glutathione S-transferases are multifunctional proteins involved in diverse intracellular events such as primary and secondary metabolisms, stress metabolism, herbicide detoxification and plant protection against ozone damages, heavy metals and xenobiotics. The plant glutathione S-transferase superfamily have been subdivided into eight classes. Phi, tau, zeta, theta, lambda, dehydroascorbate reductase and tetrachlorohydroquinone dehalogenase classes are soluble and one class is microsomal. Glutathione S-transferases are mostly soluble cytoplasmic enzymes. To date, the crystal structures of over 200 soluble glutathione S-transferases, present in plants, animals and bacteria have been resolved. The structures of glutathione S-transferase influence its function. Phylogenetic analysis suggests that all soluble glutathione S-transferases have arisen from an ancient progenitor gene, through both convergent and divergent pathways. © 2011 Academic Journals.
Journal of Theoretical Biology (10958541)281(1)pp. 18-23
The amino acid gamma-aminobutyric-acid receptors (GABAARs) belong to the ligand-gated ion channels (LGICs) superfamily. GABAARs are highly diverse in the central nervous system. These channels play a key role in regulating behavior. As a result, the prediction of GABAARs from the amino acid sequence would be helpful for research on these receptors. We have developed a method to predict these proteins using the features obtained from Chou's pseudo-amino acid composition concept and support vector machine as a powerful machine learning approach. The predictor efficiency was assessed by five-fold cross-validation. This method achieved an overall accuracy and Matthew's correlation coefficient (MCC) of 94.12% and 0.88, respectively. Furthermore, to evaluate the effect and power of each feature, the minimum Redundancy and Maximum Relevance (mRMR) feature selection method was implemented. An interesting finding in this study is the presence of all six characters (hydrophobicity, hydrophilicity, side chain mass, pK1, pK2 and pI) or combination of the characters among the 5 higher ranked features (pk2 and pI, hydrophobicity and mass, pk1, hydrophilicity and mass) obtained from the mRMR feature selection method. The results show a biologically justifiable ranked attributes of pk2 and pI; hydrophobicity, hydrophilicity and mass; mass and pk1; pk2 and mass. Based on our results, using the concept of Chou's pseudo-amino acid composition and support vector machine is an effective approach for the prediction of GABAARs. © 2011.
Journal of Structural and Functional Genomics (15700267)12(4)pp. 191-197
Matrix metalloproteinase (MMPs) and disintegrin and metalloprotease (ADAMs) belong to the zincdependent metalloproteinase family of proteins. These proteins participate in various physiological and pathological states. Thus, prediction of these proteins using amino acid sequence would be helpful. We have developed a method to predict these proteins based on the features derived from Chou's pseudo amino acid composition (PseAAC) server and support vector machine (SVM) as a powerful machine learning approach. With this method, for ADAMs and MMPs families, an overall accuracy and Matthew's correlation coefficient (MCC) of 95.89 and 0.90% were achieved respectively. Furthermore, the method is able to predict two major subclasses of MMP family; Furin-activated secreted MMPs and Type II transmembrane; with MCC of 0.89 and 0.91%, respectively. The overall accuracy for Furin-activated secreted MMPs and Type II trans-membrane was 98.18 and 99.07, respectively. Our data demonstrates an effective classification of Metalloproteinase family based on the concept of PseAAC and SVM. © Springer Science+Business Media B.V. 2011.
Electronic Journal of Environmental, Agricultural and Food Chemistry (15794377)10(6)pp. 2404-2412
The effects of cadmium toxicity and alleviation by calcium in 14-day-old maize seedlings were investigated. The seedlings treated with cadmium at concentration of 100 μM for eight days. Applications of 10 and 20 mM calcium were able to diminish cadmium toxicity through some mechanisms. The alleviation demonstrated through reduction in lipid peroxidation, anthocyanin content, proline content and cadmium uptake and rising in leaf chlorophyll and cartenoid compared to cadmium treatment, significantly.
Medicinal Chemistry (15734064)6(2)pp. 100-107
Polyketides are secondary metabolites of microorganisms synthesized by serialized reactions of a set of enzymes called polyketide synthases (PKS). As many infectious microorganisms are acquiring tolerance to antibiotics, the need for novel medicines is increasing. Recently, various methods are being used for drug discovery, including gene manipulation for biosynthesis of antibiotics such as polyketides. Due to their importance as drugs, the volume of data on polyketides is rapidly increasing. In the present paper, by using SEARCHPKS and ASMPKS servers, domain identification, and domain organization, substrate specificity of AT domain, domain assembly and chemical moiety of three Actinomycetes i.e., Mycobacterium abscessus, Micromonospora chalcea and Streptomyces achromogenes are analyzed. So far, no secondary metabolite of any of these bacteria is known. Here, it was demonstrated that KR1, KR2 and KR3 domains from M. chalcea, KR5 domain from M. abscessus and KR6 domain from S. achromogenes could be assigned as B1-type, while KR4 domain from M. abscessus and KR7 domain from S. achromogenes could be assigned as A1 type. Substrate specificity of AT1 and AT2 of M. abscessus predicted to be malonate. AT2 domain of PKS protein from S. achromogenes also selected as malonate. Methylmalonate substrate was predicted for AT1 and AT3 domains. All of the AT domains in modules of PKS protein of M. chalcea were predicted to be specific for methylmalonate. Analysis of folding rate of these proteins showed that the logarithm of (kf) decreased in proportion to protein chain length. We have also performed a comprehensive phylogenetics analysis of AT and DH domains with FabA, FabZ and dehydratase proteins of various bacteria and secondary metabolites. The phylogenetic tree derived from these sequences reflects the long joint evolution process. © 2010 Bentham Science Publishers Ltd.
Interdisciplinary Sciences - Computational Life Sciences (19132751)2(4)pp. 367-372
Infection by human papillomavirus type 16 (HPV-16) is the cause of 50% or more of cervical cancers in women. The E7 oncoprotein of HPV-16 has long been known as a potent immortalizing and transforming agent. We used different servers like PseAAC, MHC_binding, MHC_II_binding and Expasy for the present computational prediction. The results for T cell epitopes showed that B1501, A0203, A0201, A0202, A6801 and DRB0405 alleles had lower IC50 than other alleles. We also predicted several peptides with the best binding affinities for alleles of the most frequent MHC class I and II alleles of the various ethnic groups living in the different region of Iran. Two peptides (26-35) and (44-52) were predicted as B-cell epitopes. According to this analysis 1 N-glycosylation site, 2 PKC sites, 4 CK2 sites and 3 disulfide sites were predicted. Our computational study predicted that B cell epitope 1 was Casein kinase II phosphorylated (site No. 31) and glycosylated (site No. 29). Putative MHC-I epitopes 3 and 5 and MHC-II epitopes 19, 21 and 26 were predicted to be casein kinase II phosphorylated. MHC-II epitopes 19 and 21 was predicted to be glycosylated. T cell epitopes 1, 13, 16 and 24 were demonstrated to be kinase C phosphorylated. The result of this analysis for Iranian HPV-16 E7 also indicated that 21.43%, 18.37% and 60.20% of the protein were in the α-helix, extended strand and random coil respectively. © 2010 International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg.
Protein And Peptide Letters (09298665)17(10)pp. 1207-1214
There are different types of cyclins, which are active during the cell cycle and enable cyclin-dependent kinases to phosphorylate different substrates. Since there is not much similarity between amino acid sequences of cyclins, predicting these proteins is an important job. This paper presents a bioinformatics classifier to predict cyclins based on Chou's pseudo amino acid composition. Analysis of the results by StAR, which is a program for the analysis of ROC curves, showed that accuracy of the approach was 83.53% (AUC=89.44%). The present work demonstrates that the method can provide useful information for predicting cyclins. © 2010 Bentham Science Publishers Ltd.
Journal of Theoretical Biology (10958541)263(2)pp. 203-209
High-risk types of human papillomaviruses (HPVs) are the etiological agents in nearly all cases (99.7%) of cervical cancer, and the HPV E6 protein is one of the two viral oncoproteins which is expressed in virtually all HPV-positive cancers. Therefore, classifying the risk type of HPVs is very useful and necessary for diagnosis and remedy of cervical cancer. To predict and to classify the risk types of HPV by bioinformatics analysis, 96 E6 protein sequences from available databases were obtained. To investigate the risk type of these sequences, PseAAC server, ROC curves and statistical analysis were applied. Our classification was based on some characters of HPV E6 proteins, such as hydrophobicity, hydrophilicity, side chain mass, PK of the α-COOH group, PK of the α-NH3+ group and PI at 25°C. Risk type of 4 unknown HPV types and 25 non-reported HPV types were also predicted. These results show that bioinformatics based theoretical approaches can direct and simplify experimental studies. © 2009 Elsevier Ltd.
EXCLI Journal (16112156)8pp. 190-194
Glutathione S-transferase is a family of multifunctional detoxification enzymes which are mainly cytosolic that detoxify natural and exogenous toxic compounds by conjugation with glutathione. Glutathione, an endogenous tripeptide, is important as either a reducing agent or a nucleophilic scavenger. This molecule alleviates the chemical toxicity in plants by reaction of glutathione S-transferase, and its conjugates can be transported to vacuole or apoplast. The plant soluble glutathione S-transferases grouped today into seven distinct Phi, Tau, Zeta, Theta, lambda, dehydroascorbate reductase, and tetrachlorohydroquinone dehalogenase classes. In this study, bioinformatics analysis of glutathione S-transferase gene in barley was carried out using Tau-class of barley glutathione S-transferase sequences in NCBI GenBank and isolated sequence. DNA extraction, primer design, PCR, electrophoresis, column purifica-tion, DNA sequencing and analysis by some software led to identify new sequences of Tau-class of glutathione S-transferase from barley, which is similar to Tau GST of the diploid wheat. Comparison of the deduced amino acid sequences of the three barley GST genes showed that they have 99% identity with each other but only 45% identity with the new GST. This sequence was submitted to NCBI GenBank with FI131240 accession number.
Protein And Peptide Letters (09298665)16(9)pp. 1017-1023
Since there are not much experimental data available about different structural properties of Isfahan virus (ISFV), in the present investigation, computational study of G protein of ISFV was performed and the results were compared with G proteins of Chandipura virus (CHPV) and Piry virus (PV).Calculation of amino acid compositions of G proteins of viruses was done by PseAAC server.Predictions of localization, sequence of signal peptides, C, N and O glycosylation sites, transmembrane helices, cysteine bond positions and B cell epitopes of G proteins were performed by Virus- PLoc, Signal-CF, EnsembleGly, MemBrain, DiANNA and BCPREDS servers respectively.Similarities and differences between these glycoproteins were predicted and discussed. © 2009 Bentham Science Publishers Ltd.
Genomics, Proteomics And Bioinformatics (16720229)7(3)pp. 87-95
Leishmania is associated with a broad spectrum of diseases, ranging from simple cutaneous to invasive visceral leishmaniasis. Here, the sequences of ten cysteine proteases of types A, B and C of Leishmania major were obtained from GeneDB database. Prediction of MHC class I epitopes of these cysteine proteases was performed by NetCTL program version 1.2. In addition, by using BcePred server, different structural properties of the proteins were predicted to find out their potential B cell epitopes. According to this computational analysis, nine regions were predicted as B cell epitopes. The results provide useful information for designing peptide-based vaccines. © 2009 Beijing Genomics Institute.
Asian Pacific Journal of Cancer Prevention (15137368)9(4)pp. 631-636
Human papillomaviruses (HPVs) are small DNA tumor viruses that replicate and assemble exclusively in the nucleus. Thus their proteins, including E6, must carry nuclear localization signals (NLSs) to enter the nucleus. To analyze and to predict the nuclear localization signals and several post translational modifications by bioinformatics analysis, we obtained 91 E6 protein sequences from available databases. To investigate the localization of these sequences, we used Hum-Ploc software. Homology and alignment of sequences were performed by Blast software and Multalin server respectively. Prediction of N-glycosylation and serine, threonine and tyrosine phosphorylation sites of HPV E6 protein sequences was accomplished with NetNGlyc and NetPhos software. Out of 91 types, the NLSs of 29 types were predicted by signal-3L and signal-CF software. We tried to predict the NLSs of remaining HPV E6 proteins according to the homology of the already predicted NLSs. However, because of considerable variation between E6 protein sequences, we could not classify the NLSs in monopartite or bipartite. According to the results, all NLSs of HPV E6 proteins could be assigned to 11 categories. NLSs of several HPV E6 protein sequences were also determined by experimental studies. Overall, different types of HPV E6 protein in same category show approximately similar pattern in post translational modifications such as N-glycosylation and phosphorylation. Some HPV "early"genes, such as E6, are known to act as oncogenes that promote tumor growth and malignant transformation. Thus more detailed recognition of nuclear localizing sequences and nucleocytoplasmic transport pathway can play a key role in prevention and treatment of HPV infection and related cancers. The results also show that bioinformatics technology can direct and simplify experimental studies.
Mohammadzadegan, R.,
Mohabatkar, H.,
Sheikhi, M.H.,
Safavi, A.,
Khajouee, M.B. Physica E: Low-Dimensional Systems and Nanostructures (13869477)41(1)pp. 142-145
We have developed simple methods of reproducibly creating deoxyribonucleic acid (DNA)-templated gold nanowires on silicon. First DNA nanowires were aligned on silicon surfaces. Briefly, modified silicon wafer was soaked in the DNA solution, and then the solution was removed using micropipettes; the surface tension at the moving air-solution interface is sufficient to align the DNA nanowires on the silicon wafer. In another attempt, an aqueous dispersion of sodium azide-stabilized gold nanoparticles was prepared. The nanoparticles aligned double-stranded λ-DNA to form a linear nanoparticle array. Continuous gold nanowires were obtained. The above nanowires were structurally characterized using scanning electron microscopy. The results of the characterizations show the wires to be 57-323 nm wide, to be continuous with a length of 2.8-9.5 μm. The use of DNA as a template for the self-assembly of conducting nanowires represents a potentially important approach in the fabrication of nanoscale interconnects. © 2008 Elsevier B.V. All rights reserved.
Journal of Applied Animal Research (09741844)34(2)pp. 179-180
Fortyfive adult male rats (220-250g) were divided into 3 equal groups. Rats of group 1 were exposed to 50Hz, 500jiT in solenoid 10 hi day for 2 mo, group 2 were kept in condition similar to the group 1 except in off solenoid and group 3 were kept in normal condition of animal room. Serum glucose of the EMF exposed group was significantly higher and their weight gain, serum insulin and cholesterol were less than those of other groups. These findings demonstrated the potential role of EMF for clinical use. © GSP, India.
Mansoori e.g., ,
Zolghadri m.j., ,
Katebi s.d., ,
Mohabatkar, H.,
Boostani r., ,
Sadreddini m.h., Iranian Journal Of Fuzzy Systems (17350654)5(2)pp. 21-33
This paper considers the generation of some interpretable fuzzy rules for assigning an amino acid sequence into the appropriate protein superfamily. Since the main objective of this classifier is the interpretability of rules, we have used the distribution of amino acids in the sequences of proteins as features. These features are the occurrence probabilities of six exchange groups in the sequences. To generate the fuzzy rules, we have used some modified versions of a common approach. The generated rules are simple and understandable, especially for biologists. To evaluate our fuzzy classifiers, we have used four protein superfamilies from UniProt database. Experimental results show the comprehensibility of generated fuzzy rules with comparable classification accuracy.
Protein And Peptide Letters (09298665)15(3)pp. 280-285
Plant profilins form a well-known panallergen family responsible for cross-sensitization between plant foods and pollens. We sought to map T and B-cell epitopes on the Iranian Crocus sativus profilin by bioinformatics tools. The predicted peptides are useful for further vaccine development. © 2008 Bentham Science Publishers Ltd.
Pakistan Journal of Biological Sciences (18125735)10(23)pp. 4295-4298
In the present study, T-cell epitopes of gp120 of an Iranian isolate have been compared to different subtypes of HIV-1. At first, the amino acid sequences of gp120 were fetched from data banks. Then T-cell epitopes, disulfide bonding states, protein kinase C phosphorylation sites, cAMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites, N-myristoylation sites and amidation sites were predicted using different soft wares. According to this computational analysis 6 good disulfide binding states in Iranian gp120 were predicted. From the viewpoint of cAMP-dependent protein kinase phosphorylation site (1 site) Iranian isolate was similar to clades B and F. Like subtype C 1 amidation site was predicted in the Iranian subtype. In the Iranian isolate 7 sites protein kinase C phosphorylation sites and 4 N-myristoylation sites were predicted. Since the number of individuals infected with HIV-1 in Iran, like many other countries is increasing, study of similarities and differences between the Iranian samples and different clades of HIV-1 can help us in identification of the origin and understanding the changes in the virus. © 2007 Asian Network for Scientific Information.
Nanoscale Research Letters (1556276X)2(1)pp. 24-27
Computer-aided design plays a fundamental role in both top-down and bottom-up nano-system fabrication. This paper presents a bottom-up nano-filter patterning process based on DNA self-assembly. In this study we designed a new method to construct fully designed nano-filters with the pores between 5 nm and 9 nm in diameter. Our calculations illustrated that by constructing such a nano-filter we would be able to separate many molecules.
Asian Pacific Journal of Cancer Prevention (15137368)8(4)pp. 602-606
HPV-16 is the HPV most often linked to cervical carcinoma. E6 of the HPV-16 which expressed early in cancer cells is a target for immune therapeutic methods. In the present study, after fetching the sequence of HPV-16 E6 (accession No: ABC48950) from NCBI databank, by using hydrophilicity, flexibility, accessibility, turns, exposed surface, polarity and antigenic propensity scales, B cell epitopes of the protein were predicted. In addition, MHCPred version 2.0 program was used to predict MHC Class I and Class II alleles. The sequences of the epitopes were also found out. According to this computer-based prediction the results from A0203 and DRB0101 reveal lower IC50 than other alleles. For A0203 allele, peptide with the best binding affinity was 25ELQTTIHDI33. For DRB0101 allele, the peptide was 39YCKQQLLRR47. Different structural features of the protein were also predicted. These features were including glycosylation, kinase C phosphorylation, Casein kinase II phosphorylation and N-myristylation sites, and disulfide bonding states. By using these computational scales and programs, 0 glycosylation, 3 kinase C phosphorylation, 2 casein kinase II phosphorylation and 1 Nmyristylation sites and 2 disulfide bonds were predicted. Development and approval of new vaccines are keys for control of cancer. Epitopes and structural features of proteins can be predicted and this information can help us in molecular and medical studies of viruses.
Soudmand-asli, A.,
Ayatollahi, S.,
Mohabatkar, H.,
Zareie, M.,
Shariatpanahi, S.F. Journal of Petroleum Science and Engineering (09204105)58(1-2)pp. 161-172
These experiments aim to investigate the microbial enhanced oil recovery (MEOR) technique in fractured porous media using etched-glass micromodels. Three identically patterned micromodels with different fracture angle orientation of inclined, vertical and horizontal with respect to the flow direction were utilized. A non-fractured model was also used to compare the efficiency of MEOR in fractured and non-fractured porous media. Two types of bacteria were employed: Bacillus subtilis (a biosurfactant-producing bacterium) and Leuconostoc mesenteroides (an exopolymer-producing bacterium). The results show that higher oil recovery efficiency can be achieved by using biosurfactant-producing bacterium in fractured porous media. Further investigation on the effect of the mentioned bacteria on oil viscosity, porous media permeability and wettability suggests that the plugging of matrix-fracture interfaces by an exopolymer is the main reason for the low performance of the exopolymer-producing bacterium. Oil viscosity reduction as well as the reduction of IFT was also found to be the reason for better microbial recovery efficiencies of biosurfactant-producing bacterium in the fractured models. © 2007 Elsevier B.V. All rights reserved.
Saudi Medical Journal (16583175)28(10)pp. 1520-1524
Objectives: To study primer sequences (1060, 1247, 1254, 1281, 1283, and 1290) for random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR). Methods: Twenty-four clinical Serratia marcescens (S. marcescens) isolates were obtained over a 6-month period from April 2002 to September 2002 from hospitals in the Fars province of Iran. Six primers were used due to S. marcescens genome properties, and RAPD-PCR was carried out. The results were subjected to unweighted pair-group method analysis using NTSYSpc 2.02. The primers were blasted with the S. marcescens genome, and the primers efficiency was estimated. Results: The results of blast primers with S. marcescens genome sequence showed that primer 1283 had the highest homology and primer 1290 had the lowest homology. Comparing the resulted dendrograms showed that the pattern of the primers to separate isolates was closely related to their sequence homology with the genome and their amount of guanine and cytosine nucleotide content. Conclusions: There are clear differences in RAPD-PCR results when different primers are used, and it is recommended to consider genomic properties of an organism to design a primer for RAPD-PCR.
Saudi Medical Journal (16583175)27(8)pp. 1121-1124
Objective: Human T-cell leukemia virus type 1 (HTLV-1) is an enveloped retrovirus, which is associated with a T-cell malignancy known as adult T-cell leukemia (ATL). Variation in the HTLV-1 envelope nucleotide sequence has been extensively documented and has been used to classify HTLV-1 isolates into different subtypes. The virus occurs in at least 3 subtypes, which have been named A, B, and C. We conducted this study to compare the antigenic proprieties of the Iranian isolate of HTLV-1 with the homologous region of different subtypes of the virus. Methods: This study took place in the Department of Biology, College of Sciences, Shiraz University, Iran in 2005. The predicted antigenic sites and secondary structure of the envelope glycoprotein of HTLV-1, present in Iran, have been compared with the antigenic sites and secondary structure of the homologous domains in subtypes A, B, C of the virus. To predict the epitopes of glycoproteins, 21 different scales were used. Results: The number of helices in the Iranian isolate was equal to the number of these regions in all 3 subtypes, but the number of β-sheets was more than other viruses. One potential glycosylation site, on all these studied envelope glycoproteins, was predicted. Antigenic sites in the Iranian isolate were almost similar to subtype A of the virus and the Iranian isolate of HTLV-1 may be belongs to subtype A. Conclusion: Our results indicate the similarities and differences between the Iranian and other subtypes of HTLV-1. Antigenic sites represent potential candidates for use in a peptide vaccine against HTLV-1 glycoproteins and since most of the properties of a particular protein depend on its structural properties, this type of study can help in better understanding of HTLV-1 isolates present in Iran.
Khalafi-nezhad, A.,
Rad, M.N.S.,
Mohabatkar, H.,
Asrari z., ,
Hemmateenejad b., Bioorganic and Medicinal Chemistry (14643391)13(6)pp. 1931-1938
In view of obtaining some potential antibacterial compounds, we have described synthesis of some chloroaryloxyalkyl imidazole and benzimidazole derivatives. The relevant step in the synthetic sequence was the initial condensation of 4-chloro or 2,4-dichlorophenol with 1, n-dibromoalkanes (n = 2, 4, 5) to provide compounds 3a-f in sufficient yields. The subsequent condensation of 3a-f with some imidazole derivatives and benzimidazole afforded products 4a-l and 5a-e in good yields. Some of compounds 4a-l as well as 5a-e were tested in vitro against Salmonella typhi O-901 and Staphylococcus aureus A 15091. Compounds 4a and 4c showed considerable bactericidal activities against tested bacteria. Compound 4b showed significant activity against S. aureus A 15091 but was inactive against S. typhi O-901. Other compounds showed intermediate activities against S. aureus A 15091 but most of them were inactive against S. typhi O-901. Semiempirical AM1 calculations showed that negative electrostatic potentials around oxygen of the phenoxy and nitrogen of the imidazole moieties have direct effect on the antibacterial activity towards S. aureus A 15091. In QSAR analysis, different electronic, topologic, functional groups and physicochemical descriptors were calculated for each molecule and a three parametric equation was found between the log MIC and HOMO energy, hydration energy and number of primary carbon atoms of the molecules. © 2005 Elsevier Ltd. All rights reserved.
Iranian Biomedical Journal (2008823X)9(1)pp. 37-40
This study was conducted to determine the location of DNA segment with homology to the rat conserved genomic DNA in human chromosomes. The labeled rat genomic DNA was hybridized with normal human (male) metaphases. The study of 74 metaphases after fluorescence in situ hybridization showed 371 twin-spot signals on human chromosomes. Statistical analysis indicated that the specific accumulation of signals on 1q22-qter, 2p2, 3p21-p23, 4q3, 6q2, 8p12-pter, 11p12-pter, 11q12-qter, 12q2, 13p, 15p, 16q2, 21q12-qter, Yq1-qter, and Xq2 was not random. Results of stepwise multiple linear regressions indicated that number of mapped oncogenes (Beta = 1.092; t = 7.552; P<0.001) and density of mapped oncogenes on chromosomes (Beta = -0.832; t = -5.751; P<0.001) have significant effects on number of double-spots on human chromosomes. These data reflects the evolutionary conservation between rat DNA and human DNA at the above-mentioned bands.
Iranian Journal Of Public Health (22516085)33(2)pp. 56-59
Fibrillin is a large glycoprotein synthesized in the tissues involved in Marfan syndrome, and known to be involved in tissue elasticity. The syndrome is corresponded to fbn1 gene and is characterized by cardiovascular, ocular, and skeletal abnormalities. N-terminus of fibrillin 1 binds to microfibril-associated glycoprotein 1 (MAGP-1) in a calcium-dependent manner. In this study, the amino acid sequence of fibrillin protein of a patient with Marfan syndrome (accession No. XM- 034890) has been compared to the amino acid sequence of normal fibrillin (accession No. P-35555). In this patient, mutations causing a Gly (267) to Thr and Tyr (532) to Cys amino acids changes have been occurred. Method of Garnier was used to predict the secondary structure of the proteins and probable N-glycosylation sites were searched. Results of these analyses show no significant structural difference between the mutant and normal fibrillin proteins. Although in some cases characterization of the binding requirements has shown that a folded, secondary structure of fibrillin was necessary for binding, our results are in agreement with those findings that at least in some cases, fibrillin gene defects are not sole determinants of Marfan phenotype. © 2004, Iranian Journal of Public Health. All rights reserved.
Burns (03054179)30(8)pp. 829-832
Masjid-i-Sulaiman (MIS) is located in the southwest of Iran. Unfortunately, some parts of MIS are contaminated by subsurface leakage of natural gas containing H 2S. In order to investigate the possible effect(s) of chronic exposure to sulfur compounds on suicidal behavior, the present study was done. In the 2-year period, 561 individuals attempted suicide (260 men and 301 women). Completed suicide comprised of 19 men and 32 women. The rate per 100,000 person-years was 19.9 for men and 34.8 for women aged over 15 years. Forty-two (13 men and 29 women) of 561 patients were self-immolators by fire with a male:female ratio 0.45. This represents 22.4 burns per 100,000 person-years and is equivalent to 7.4% of all suicide attempts. Thirty-three of 42 patients died (78.6%) who were 9 men and 24 women with male:female ratio 0.37. There is statistically significant differences between sex groups (P (2) = 0.0091). The self-inflicted burn was the most frequent method for lethal suicide. Winter was the most common season for self-burning followed by spring. Statistical analysis showed significant difference between seasons for self-inflicted burn (P (2) = 0.00001). Analysis of correlation showed statistically positive correlation coefficient between mean values of all reactive sulfur compounds and seasonal frequency of suicide (r = 0.923, P (1) = 0.038). © 2004 Elsevier Ltd and ISBI. All rights reserved.
Biochemical and Biophysical Research Communications (0006291X)316(3)pp. 749-752
In order to find the effect of genetic polymorphisms of GSTM1 and GSTT1 on blood pressure of individuals chronically exposed to sulfur compounds, the present study was done. Study subjects (38 males, 38 females) were residents of contaminated areas of Masjid-i-Sulaiman (southwest of Iran). The GSTM1 and GSTT1 genotypes were determined using a polymerase chain reaction (PCR)-based method. The non-parametric Sign test was applied in order to detect differences between the GSTs genotypes of study subjects and the normal mean values according to the sex and age of subjects. From four combination of genotypes, systolic blood pressure significantly decreased in combination of null-GSTM1 and present-GSTT1 (Z=-2.41; P=0.016), and diastolic blood pressure significantly increased in combination of present-GSTM1 and null-GSTT1 (Z=+2. 14; P=0.032). It is speculated about polymorphisms of GSTs in individuals chronically exposed to natural sour gas, which contains H2S, fulfilling a physiological role(s) in regulating blood pressure. © 2004 Elsevier Inc. All rights reserved.
Pharmacology Biochemistry and Behavior (00913057)77(4)pp. 793-795
To identify whether the polymorphisms of glutathione S-transferase M1 (GSTM1) and GSTT1 genes predict a high-tended risk of using tobacco, the GSTM1 and GSTT1 genotypes of 369 Iranian males (254 nonsmokers and 115 smokers) and 314 Iranian females (245 nonsmokers and 69 smokers) were determined. The frequencies of GSTM1 (males: OR=0.98, 95% CI=0.62-1.57, P=.974; females: OR=1.34, 95% CI=0.75-2.39, P=.358) and GSTT1 (males: OR=1.25, 95% CI=0.76-2.04, P=.412; females: OR=0.84, 95% CI=0.46-1.51, P=.626) null genotypes were similar in nonsmokers and smokers. The risk of being a smoker was to be equally frequent in each combination of the genotypes. The present results revealed that there was no difference between smokers and nonsmokers for these two genetic polymorphisms. © 2004 Elsevier Inc. All rights reserved.
Brazilian Journal of Medical and Biological Research (0100879X)37(5)pp. 675-681
We describe the impact of subtype differences on the seroreactivity of linear antigenic epitopes in envelope glycoprotein of HIV-1 isolates from different geographical locations. By computer analysis, we predicted potential antigenic sites of envelope glycoprotein (gp120 and gp41) of this virus. For this purpose, after fetching sequences of proteins of interest from data banks, values of hydrophilicity, flexibility, accessibility, inverted hydrophobicity, and secondary structure were considered. We identified several potential antigenic epitopes in a B subtype strain of envelope glycoprotein of HIV-1 (IIIB). Solid-phase peptide synthesis methods of Merrifield and Fmoc chemistry were used for synthesizing peptides. These synthetic peptides corresponded mainly to the C2, V3 and CD4 binding sites of gp120 and some parts of the ectodomain of gp41. The reactivity of these peptides was tested by ELISA against different HIV-1-positive sera from different locations in India. For two of these predicted epitopes, the corresponding Indian consensus sequences (LAIERYLKQQLLGWG and DIIGDIRQAHCNISEDKWNET) (subtype C) were also synthesized and their reactivity was tested by ELISA. These peptides also distinguished HIV-1-positive sera of Indians with C subtype infections from sera from HIV-negative subjects.
Iranian Biomedical Journal (2008823X)7(3)pp. 145-145
