393 results on '"Javadmanesh A"'
Search Results
52. Evaluation of Different Signal Peptides Using Bioinformatics Tools to Express Recombinant Erythropoietin in Mammalian Cells
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Vahedi, Farid, Nassiri, Mohammadreza, Ghovvati, Shahrokh, and Javadmanesh, Ali
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- 2019
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53. Production of Phytase Enzyme by a Bioengineered Probiotic for Degrading of Phytate Phosphorus in the Digestive Tract of Poultry
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Pakbaten, Bahareh, Majidzadeh Heravi, Reza, Kermanshahi, Hassan, Sekhavati, Mohammad-Hadi, Javadmanesh, Ali, and Mohammadi Ziarat, Masoud
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- 2019
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54. Virtual water requirement of cow milk production under two different dietary strategies
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MITRA RIASI, SEYED HADI EBRAHIMI, and ALI JAVADMANESH
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Cow milk ,Ration formulation ,Water footprint ,Animal culture ,SF1-1100 - Abstract
Nutritionists have liberty to choose various feeds for formulating a balanced ration depending upon the nutritive value, availability and feed cost. Although final target in an alternative ration is to obtain similar energy, protein and other nutrients, it would be favourable to consider virtual water (VW) requirement which must be spent while making a balanced ration. This paper compared two isonitrogenous and isocaloric balanced dairy cow rations for their VW requirements. VW in the maize silage-based ration was greater than that of alfalfa and wheat straw-based diet (39.73 versus 34.45 m3). It was also found that by-product feeds such as molasses, beet sugar pulp, corn gluten, and soybean meal require a lesser amount of VW, thus, they could be the best candidates to be used as much as conventional main feeds in the ration of dairy cattle for decreasing VW requirement of milk. Using feeds with less water utilization could reduce water requirement for milk production up to 12%.
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- 2021
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55. Effect of whey powder and physical form of feed on humoral immune response and expression of interleukin-4 and interferon-gamma transcripts in jejunum of broiler chickens
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sonia zakizadeh, Maryam Torabi, Ali Javadmanesh, Ali Zanganeh, and Mohammad-Hossien Nazem-Shirazi
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lymphoid organs ,humoral immunity ,gene expression ,vaccine titration ,Agriculture ,Biotechnology ,TP248.13-248.65 - Abstract
This study was conducted to assess the effect of whey powder and physical form of feed on humoral immunity and transcript abundances of interleukin-4(IL-4) and interferon-gamma (In-γ) genes on 240 Ross-308 day-old-chickens. The experiment was conducted in a completely randomized design in 6 treatments in factorial arrangement (2×3), whey powder at three levels (0, 4,8%) and physical form in two levels (mash, pellet) in broiler chicken diet with 4 repeats and 10 chickens per replicate. The diets formulated based on nutritional requirements of Ross strain-308 (2009) and were fed to the birds in three periods. To determine the immunity titer of ND, IBV, IBD and influenza blood samples were collected at day 10, 31 and 42. At the end of periods, one chicken was selected from experimental units and slaughtered; lymphatic organs were weighted and gene expression of IL-4 and In-γ measured after mRNA extraction and cDNA synthesis. It was found that the addition of whey powder did not have a significant effect on the weights of the spleen and bursa of Fabricius, but the pelleting in the growing stage had a significant effect on the weight of spleen (p
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- 2018
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56. Investigation of allelic frequency and forensic genetics parameter for 10 STR loci in Arab and Kurd ethnics of Iran
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Mohammadreza Nassiri, Shahrokh Ghovvati, Seyed Ziaedin Mirhoseini, Ali Javadmanesh, Morteza Mahdavi, Arash Alipour, and Masoume Vakili-Azghandi
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DNA Fingerprinting ,Allelic frequencies ,Identity determination ,STR Marker ,Arab and Kurd ethnics ,Forensic genetics ,Medicine ,Medicine (General) ,R5-920 - Abstract
Background and Aim: Short tandem repeat (STR) markers, are conserved region in human genome and highly polymorphic between individuals. Nowadays, genotyping of STR marker is widely known and used for the genetic identification of individuals in forensic DNA analyses. Based on allelic frequencies of STR loci varies between populations, investigation of genetically and forensically parameters in each population and characterization of these markers is necessary. The objective of this study was to optimizing laboratory method for application of 10autosomal STR loci (TPOX، vWA، D7S820، D8S1179، D13S317، D16S539، D18S51، D5S818، THO1، D21S311) in Kurd and Arab ethnics of Iran and investigation of population and forensic genetics parameter of these markers in these populations. Materials and Methods: In this semi-experimental study, blood samples from 93 Arab and 94 Kurd individuals were collected. After DNA extraction, PCR amplification was carried out for 10 autosomal STR loci, individually. Then, acrylamide gel electrophoresis was used to determine the genotype of each individual in each site. Results: Deviation from Hardy Weinberg equilibrium even after Bonfferroni correction was seen in the locus of D13S317in both Populations. After D13S317 loci, the highest observed heterozygosity was seen in D21S311loci for Kurd population (94%) and in THO1, vWA and D5S818 locifor Arab population (84%). The lowest observed heterozygosity (0.71 and 0.72) was seen in TPOX loci for both populations form Arab and Kurd ethnics, respectively. Investigation of forensic genetic parameters (PI, PE, PD, and PIC) showed that in except of the D13S317 loci other remaining evaluated locus had proper properties for using in genetics fingertips in both of Kourd and Arab ethnics. Conclusion: The results of current study indicate that the necessity investigation of forensic genetics for rapid characterization of the different ethnicities which located in different geographic parts of Iran in order to choose the appropriate data set to calculate of forensic genetics parameters not only within each ethnic but also between them.
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- 2018
57. The immunomodulatory effects of lactoferrin and its derived peptides on NF‐κB signaling pathway: A systematic review and meta‐analysis
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Yami, Hojjat Allah, primary, Tahmoorespur, Mojtaba, additional, Javadmanesh, Ali, additional, Tazarghi, Abbas, additional, and Sekhavati, Mohammad Hadi, additional
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- 2023
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58. Effects of cLFchimera peptide on intestinal morphology, integrity, microbiota, and immune cells in broiler chickens challenged with necrotic enteritis
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Daneshmand, Ali, Kermanshahi, Hassan, Sekhavati, Mohammad Hadi, Javadmanesh, Ali, Ahmadian, Monireh, Alizadeh, Marzieh, and Aldawoodi, Ahmed
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- 2020
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59. Rumen‐protected l‐carnitine supplementation during mating period altered metabolic status and reproductive performance of ewes.
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Masoomi, Maziar, Kheirandish, Parisa, Javadmanesh, Ali, Danesh Mesgaran, Sadjad, Izadi, Hooman, and Danesh Mesgaran, Mohsen
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EWES ,CARNITINE ,TOLL-like receptors ,DIETARY supplements ,BLOOD collection ,RUMEN fermentation ,GENE expression - Abstract
Current study hypothesized that dietary l‐carnitine (LC) inclusion during the mating period ameliorates both metabolic status and reproductive performance of ewes. Seventy Baluchi ewes (52 ± 4.2 kg of bodyweight and 18 ± 6 months old of age) were enrolled in this study. Animals were randomly allocated into two dietary treatments, control (only basal diet) or basal diet plus supplementation with a rumen‐protected LC (Carneon 20 Rumin‐pro; 20% LC; Kaesler Nutrition GmbH) at the rate of 10 g/head/day from 21 days before until 35 days after introducing rams to the ewes (MP). Feed intake was monitored by subtracting the ort from feed offered. Blood sample collection was conducted on Days −10, +10 and +20 relative to MP. Pregnancy was confirmed on Day 30 post‐MP. Feed intake of the ewes in the LC group was higher than the control (p < 0.05). LC supplementation increased the cholesterol concentration in the ewes (p < 0.05). Blood urea concentration of animals in the LC group was significantly lower than the control (p < 0.05). The mRNA expression of toll‐like receptor 4 was evidently lower in animals supplemented with LC than the control (p < 0.05). Both lambing and fecundity rates in the LC group tended to be higher compared with the control. LC supplementation showed potential to alter certain metabolites in the ewes. A tendency for higher lambing rate may partly be driven by dams efficient energy partitioning to support foetal growth and maintaining pregnancy. [ABSTRACT FROM AUTHOR]
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- 2024
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60. One intron variant in the oocyte expressed protein (OOEP) gene is associated with twinning rate, prolificacy, and several body measurement traits in Awassi ewes
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Khazaal, Neam M., primary, Alghetaa, Hasan F.K., additional, Alkhammas, Ahmed H., additional, Al-Thuwaini, Tahreer M., additional, Javadmanesh, Ali, additional, Aljubouri, Thamer R.S., additional, and Al-Shuhaib, Mohammed Baqur S., additional
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- 2023
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61. Differential Expression of RNAseq Imprinted Genes from Bovine Females Before and After Puberty
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Keyvan Karami, Saeed Zerehdaran, and Ali Javadmanesh
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Genetics ,General Medicine ,Molecular Biology ,Biochemistry ,Ecology, Evolution, Behavior and Systematics - Published
- 2023
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62. Antimicrobial peptide, cLF36, affects performance and intestinal morphology, microflora, junctional proteins, and immune cells in broilers challenged with E. coli
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Daneshmand, Ali, Kermanshahi, Hassan, Sekhavati, Mohammad Hadi, Javadmanesh, Ali, and Ahmadian, Monireh
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- 2019
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63. The Effect of Physical Activity and Gender on Self-Esteem of Shiraz University Students
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Robabeh Rostami, Hossein Mohamad- Sadeghi Poor, and Mohammad Javadmanesh
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self-esteem ,Physical Activities ,Gender ,Nursing ,RT1-120 ,Medicine (General) ,R5-920 - Abstract
Introduction: Many studies have shown that social interactions resulting from participation in physical activities lead to an optimal state of self-esteem. The findings of previous research on gender differences regarding this factor, however, have not been consistent. In an attempt to fill this gap, this study is designed to investigate the effect of physical activity and gender on students' self-esteem in Shiraz University. Methods: Random-Comparative method was employed to conduct this research. Population included all undergraduate students of Shiraz University. Participants were selected through random cluster sampling. 332 students filled out a Cooper Smith and Colleague’s Questionnaire and the scores of 218 of them were analyzed. Two-way analysis of variance was administered for the analysis (P≤0.05). Results: The results conveyed that the major impact of gender (P=0.05) and physical activity (P=0.02) on self-esteem were both significant. Active students had higher self-esteem compared to inactive ones (P=0.02) and the self-esteem scores of female students were higher than male students (P=0.05). Conclusion: The results of this research indicate that participation in physical activities may improve the self- esteem of bachelor students studying in Shiraz University. Furthermore, the analysis of the results showed that female students enjoyed higher self- esteem.
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- 2016
64. Effect of in ovo injection of threonine on Mucin2 gene expression and digestive enzyme activity in Japanese quail (Coturnix japonica)
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Kermanshahi, H., Daneshmand, A., Emami, N. Khodambashi, Tabari, D. Ghofrani, Doosti, M., Javadmanesh, A., and Ibrahim, S.A.
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- 2015
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65. Genetic Indications for Anadromous Hilsa Shad (Tenualosa ilisha) in Shatt Al-Arab River Using mtDNA Cytochrome B Gene
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Taqi A. Abdullah, Ali Javadmanesh, and Sajed S. H. Al-Noor
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Animal Science and Zoology ,Horticulture ,Pollution ,Agronomy and Crop Science ,Biochemistry - Abstract
Hilsa species are broadly described as largely anadromous fish with a large valuable population size. It is well-known as one of the most critical commercial and occurs in marine, estuarine and riverine environments Hilsa shad, Tenualosa ilisha locally known as Sbour, migrates to the freshwater environment of the Shatt Al-Arab River systems for breeding. It was determined the genetic variation in 70 specimens of T. ilisha from four sites at the Shatt Al-Arab River, the mtDNA cytochrome-b gene was selected as a molecular marker for detecting genetic diversity, origin, and divergence of the population through comparing them with 6 samples from different locations at Indo-Pacific. The AMOVA analysis showed that the variation between groups is 60.97% and 39.02% within population indicating statistically significant P value (P
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- 2022
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66. Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches.
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Keyvan Karami, Saeed Zerehdaran, Ali Javadmanesh, Mohammad Mahdi Shariati, and Hossein Fallahi
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Medicine ,Science - Abstract
Genomic imprinting results in monoallelic expression of genes in mammals and flowering plants. Understanding the function of imprinted genes improves our knowledge of the regulatory processes in the genome. In this study, we have employed classification and clustering algorithms with attribute weighting to specify the unique attributes of both imprinted (monoallelic) and biallelic expressed genes. We have obtained characteristics of 22 known monoallelically expressed (imprinted) and 8 biallelic expressed genes that have been experimentally validated alongside 208 randomly selected genes in bovine (Bos taurus). Attribute weighting methods and various supervised and unsupervised algorithms in machine learning were applied. Unique characteristics were discovered and used to distinguish mono and biallelic expressed genes from each other in bovine. To obtain the accuracy of classification, 10-fold cross-validation with concerning each combination of attribute weighting (feature selection) and machine learning algorithms, was used. Our approach was able to accurately predict mono and biallelic genes using the genomics and proteomics attributes.
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- 2019
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67. Beneficial worm allies warn plants of parasite attack below‐ground and reduce above‐ground herbivore preference and performance
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Javad Karimi, Monireh Cheniany, Mohammad Zakiaghl, Ali Javadmanesh, Alireza Seifi, Tina Kyndt, Lukasz L. Stelinski, Javad Asili, Shokoofeh Kamali, Mojtaba Hosseini, and Mahyar Heydarpour
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biology ,Host (biology) ,fungi ,Biological pest control ,food and beverages ,biology.organism_classification ,Plant Roots ,Solanum lycopersicum ,Botany ,Heterorhabditis bacteriophora ,Genetics ,Plant defense against herbivory ,Animals ,Root-knot nematode ,Parasites ,Tuta absoluta ,Herbivory ,Tylenchoidea ,Ecology, Evolution, Behavior and Systematics ,Systemic acquired resistance ,Meloidogyne javanica - Abstract
Antagonistic interactions among different functional guilds of nematodes have been recognized for quite some time, but the underlying explanatory mechanisms are unclear. We investigated responses of tomato (Solanum lycopersicum) to two functional guilds of nematodes - plant parasite (Meloidogyne javanica) and entomopathogens (Heterorhabditis bacteriophora, Steinernema feltiae belowground, and S. carpocapsae) - as well as a leaf mining insect (Tuta absoluta) aboveground. Our results indicate that entomopathogenic nematodes (EPNs): 1) reduced root knot nematode (RKN) infestation belowground, 2) reduced herbivore (T. absoluta) host preference and performance aboveground, and 3) induced overlapping plant defense responses by rapidly activating polyphenol oxidase (PPO) and guaiacol peroxidase (GP) activity in roots, but simultaneously suppressing this activity in aboveground tissues. Concurrently, we investigated potential plant signaling mechanisms underlying these interactions using transcriptome analyses. We found that both entomopathogens and plant parasites triggered immune responses in plant roots with shared gene expression. Secondary metabolite transcripts induced in response to the two nematode functional guilds were generally overlapping and showed an analogous profile of regulation. Likewise, we show that EPNs modulate plant defense against RKN invasion, in part, by suppressing active expression of antioxidant enzymes. Inoculations of roots with EPN triggered an immune response in tomato via up-regulated phenylpropanoid metabolism and synthesis of protease inhibitors (PIs) in plant tissues, which may explain decreased egg laying and developmental performance exhibited by herbivores on EPN-inoculated plants. Furthermore, changes induced in the volatile organic compound (VOC)-related transcriptome indicated that M. javanica and/or S. carpocapsae inoculation of plants triggered both direct and indirect defenses. Our results support the hypothesis that plants 'mistake' subterranean EPNs for parasites, and these otherwise beneficial worms activate a battery of plant defenses associated with systemic acquired resistance (SAR) and/or induced systemic resistance (ISR) with concomitant antagonistic effects on temporally co-occurring subterranean plant pathogenic nematodes and terrestrial herbivores.
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- 2021
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68. Identification of selection signatures in Capra hircus and Capra aegagrus in Iran
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Taheri, Sadegh, primary, Saedi, Naghmeh, additional, Zerehdaran, Saeed, additional, and Javadmanesh, Ali, additional
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- 2023
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69. Investigating the Probiotic Properties and Antimicrobial Activity of Lactic Acid Bacteria Isolated from an Iranian Fermented Dairy Product, Kashk
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Saboori, Bahareh, primary, Shahidi, Fakhri, additional, Hedayati, Sara, additional, and Javadmanesh, Ali, additional
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- 2022
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70. Evaluation of antioxidant, antibacterial and cytotoxicity activities of exopolysaccharide from Enterococcus strains isolated from traditional Iranian Kishk
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Paria Rahnama Vosough, Ali Javadmanesh, Mohammad Reza Edalatian Dovom, Mohammad Najafi, Baltasar Mayo, and Ferdowsi University of Mashhad
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Antioxidant ,DPPH ,Cytotoxicity ,General Chemical Engineering ,medicine.medical_treatment ,Antimicrobial activity ,medicine.disease_cause ,Industrial and Manufacturing Engineering ,Kishk ,chemistry.chemical_compound ,Antioxidant activity ,Listeria monocytogenes ,medicine ,Food science ,Safety, Risk, Reliability and Quality ,Antibacterial agent ,biology ,Chemistry ,Pathogenic bacteria ,Antimicrobial ,biology.organism_classification ,Enterococcus ,Staphylococcus aureus ,Food Science - Abstract
In this study, the antimicrobial effect of exopolysaccharide (EPS) extracted from Enterococcus strains [E. durans K48 (MT437,248), E. faecium R114 (MT437,249) and E. faecium T52 (MT437,250)] isolated from Kishk was applied against some foodborne pathogenic bacteria using well diffusion and microdilution methods. The antioxidant activity of EPS was also evaluated by 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging assay and ferric reducing antioxidant power (FRAP) method. The cytotoxicity effect of EPS on human Gingival Fibroblast (HGF) cell line was also assessed. The results obtained by antimicrobial test showed that the most resistant bacteria to the examined EPS was Listeria monocytogenes, and the most susceptible were Staphylococcus aureus and E. faecalis. The results showed that the DPPH inhibitory percentage of EPS (25 mg/mL) from E. durans K48, E. faecium R114, and E. faecium T52 was 53%, 58% and 64%, respectively. EPS from E. faecium T52 displayed the highest reducing power, but statistically, there was no significant difference between the reducing power of EPS T52 and EPS R114 (P ≥ 0.05). The lowest toxicity percentage of EPS k48, EPS T52, and EPS R114 on normal human cell line at a concentration of 0.2 mg/mL was 10%, 15%, and 13%, respectively, which was statistically significant (P < 0.05). The obtained results in the present study indicate that EPS from the examined LAB strains with no in vitro cytotoxicity can be a potential source of natural antioxidant and antibacterial agent to be used in food and pharmaceutical industries., This work was financially supported by a Grant (No. 47333) from Ferdowsi University of Mashhad (Research affairs), Iran.
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- 2021
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71. Isolation and Identification of Yellow Spot Causing Microbial Agents on Chicken Sausage Based on Culture and Molecular Methods
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Ali Javadmanesh, Fakhri Shahidi, Seyed Ali Mortazavi, Atefeh Soradeghi Toopkanloo, Mohammad Javad Varidi, and Sahar Roshanak
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Chemistry ,Identification (biology) ,Isolation (microbiology) ,Food Science ,Microbiology - Published
- 2021
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72. Atlas of tissue- and developmental stage specific gene expression for the bovine insulin-like growth factor (IGF) system.
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Mani Ghanipoor-Samami, Ali Javadmanesh, Brian M Burns, Dana A Thomsen, Greg S Nattrass, Consuelo Amor S Estrella, Karen L Kind, and Stefan Hiendleder
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Medicine ,Science - Abstract
The insulin-like growth factor (IGF) axis is fundamental for mammalian growth and development. However, no comprehensive reference data on gene expression across tissues and pre- and postnatal developmental stages are available for any given species. Here we provide systematic promoter- and splice variant specific information on expression of IGF system components in embryonic (Day 48), fetal (Day 153), term (Day 277, placenta) and juvenile (Day 365-396) tissues of domestic cow, a major agricultural species and biomedical model. Analysis of spatiotemporal changes in expression of IGF1, IGF2, IGF1R, IGF2R, IGFBP1-8 and IR genes, as well as lncRNAs H19 and AIRN, by qPCR, indicated an overall increase in expression from embryo to fetal stage, and decrease in expression from fetal to juvenile stage. The stronger decrease in expression of lncRNAs (average -16-fold) and ligands (average -12.1-fold) compared to receptors (average -5.7-fold) and binding proteins (average -4.3-fold) is consistent with known functions of IGF peptides and supports important roles of lncRNAs in prenatal development. Pronounced overall reduction in postnatal expression of IGF system components in lung (-12.9-fold) and kidney (-13.2-fold) are signatures of major changes in organ function while more similar hepatic expression levels (-2.2-fold) are evidence of the endocrine rather than autocrine/paracrine role of IGFs in postnatal growth regulation. Despite its rapid growth, placenta displayed a more stable expression pattern than other organs during prenatal development. Quantitative analyses of contributions of promoters P0-P4 to global IGF2 transcript in fetal tissues revealed that P4 accounted for the bulk of transcript in all tissues but skeletal muscle. Demonstration of IGF2 expression in fetal muscle and postnatal liver from a promoter orthologous to mouse and human promoter P0 provides further evidence for an evolutionary and developmental shift from placenta-specific P0-expression in rodents and suggests that some aspects of bovine IGF expression may be closer to human than mouse.
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- 2018
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73. Iranian kishk as a source of lactic acid bacteria producing exopolysaccharide
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Edalatian, Mohammad Reza, Vosough, Paria Rahnama, Habibi Najafi, Mohammad Bagher, Javadmanesh, Ali, and Mayo Pérez, Baltasar
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Exopolysaccharide ,Lactic acid bacteria ,Kishk - Abstract
Trabajo presentado en el XIII International Scientific Agriculture Symposium AGROSYM 2022, celebrado en Sarajevo (Bosnia y Herzegovina), del 6 al 9 de octubre de 2022, Exopolysaccharides are high molecular weight polymers composed of sugar subunits. Produced exopolysaccharides by lactic acid bacteria (LAB) play a significant role in improvement of organoleptic properties of fermented dairy products such as yogurt. Diversely, the probiotic function of these bacteria and the prebiotic properties of their produced biopolymers promote consumer¿s health. For this purpose, a traditional dairy product known as ¿Kishk¿ was selected. 143 strains of lactic acid bacteria were isolated from Iranian Kishk in Khorasan Province and cultured in formulated MRS mediums with different sugars such as glucose, fructose, sucrose and, lactose (40 g/L) and incubated in anaerobic conditions at 30 and 37°C for 48 hours. The microscopic features of the isolates were assessed and the production of exopolysaccharide in the culture medium was evaluated by disk and ruthenium red methods. The phenol-sulfuric and weight method were used to quantify exopolysaccharide production. Results showed pH of Kishk samples ranged from 3.60 to 4.08 and the average of total mesophilic count and LAB count of samples were 6.50 and 5.89 log CFU/g, respectively. Analysis of data exhibited 79 out of 143 lactic acid bacteria isolates were exopolysaccharide producer and 70% of them were cocci. The average of maximum and minimum production by weight method were 2.61 g/L and 0.08 g/L, respectively. The average of highest and the lowest amount of exopolysaccharide by phenol sulfuric method were measured 1.87 g/L and 0.06 g/L, respectively. This study indicates the potential of exopolysaccharide production by Iranian native species from dairy products.
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- 2022
74. Interactive effect of exercise training and growth hormone administration on histopathological and functional assessment of the liver in male Wistar rats
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RASHIDLAMIR, Amir, primary, ROOZBEH, Behnam, additional, BAGHERI, Reza, additional, MOAZZAMI, Mahtab, additional, MOOSAVI, Zahra, additional, JAVADMANESH, Ali, additional, BAKER, Julien S., additional, and WONG, Alexei, additional
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- 2022
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75. One intron variant in the oocyte expressed protein (OOEP) gene is associated with twinning rate, prolificacy, and several body measurement traits in Awassi ewes
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Neam M. Khazaal, Hasan F.K. Alghetaa, Ahmed H. Alkhammas, Tahreer M. Al-Thuwaini, Ali Javadmanesh, Thamer R.S. Aljubouri, and Mohammed Baqur S. Al-Shuhaib
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Food Animals ,Animal Science and Zoology - Published
- 2023
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76. A DNA methylation panel for high performance detection of colorectal cancer
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Mohammad Amin Kerachian, Mahdi Zardadi, Marjan Azghandi, Khadijeh Jamialahmadi, Ali Javadmanesh, and Ehsan Shams Davodly
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Male ,Oncology ,Cancer Research ,medicine.medical_specialty ,Colorectal cancer ,In silico ,Biology ,Sensitivity and Specificity ,Likelihood ratios in diagnostic testing ,03 medical and health sciences ,0302 clinical medicine ,Aldehyde Reductase ,Internal medicine ,Genetics ,medicine ,Humans ,Epigenetics ,Molecular Biology ,Cancer ,Methylation ,DNA Methylation ,Middle Aged ,medicine.disease ,Genetic marker ,030220 oncology & carcinogenesis ,Diagnostic odds ratio ,Female ,Colorectal Neoplasms ,Septins - Abstract
One of the most promising ways to diagnose cancer especially colorectal cancer (CRC) is to trace its epigenetic events. In this article, a discovery step for detection of methylated DNA markers (MDMs) was performed using SureSelectXT Methyl-Seq in CRC case and control groups in addition to several methylation profiling datasets (GSE48684, GSE53051, GSE77718, GSE101764, and GSE42752). In silico validation of MDMs in colorectal and other cancers was conducted by Lnc2met. MethyLight assay was run on 40 and 47 case and control formalin-fixed paraffin-embedded tissues, respectively and the performance of selected genes were classified by support vector machine (SVM). As a result, 180 regions were identified among all common genes. In addition to SEPT9 and SFRP2, the best three MDM regions were selected from SLC30A10, AKR1B1 and GALNT14. Based on all assays, the best performance was accomplished by SEPT9/AKR1B1 with 98% sensitivity, 99% specificity, 125 positive likelihood ratio, 0.02 negative likelihood ratio and 5074 diagnostic odds ratio. Our results indicate that the AKR1B1/SEPT9 methylation panel detects CRC with a higher performance than SEPT9 methylation, which is a commercial diagnostic test for CRC. However, the creation of a clinically valuable test derived from this study requires performance evaluation in liquid biopsies.
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- 2021
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77. Effect of Abiotic Stresses on Histidine kinases Gene Expression in Zea mays L. cv. SC. 704
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Javadmanesh, Susan, Rahmani, Fatemeh, and Pourakbar, Latifeh
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drought stress ,RT-PCR ,salinity stress ,UV-B radiation ,ZmHKs gene expression ,Biochemistry ,QD415-436 - Abstract
UV-B radiation and osmotic stress (like drought and salinity) have a significant effect on physiology, morphology, biochemistry and molecular biology. To cope with such stimuli, plants must be able to effectively sense, respond to and adapt to changes in their biological activities. Hence, signal transduction pathways play important role in response to environmental stimuli. In this study, the expression of three Histidine Kinases including ZmHK1, ZmHK2 and ZmHK3a was studied in maize plants exposed to 8 days drought, salinity and UV-B stresses applying transcript approach. The semi-quantitative RT-PCR analyses of ZmHKs showed up-regulation of ZmHK1 and ZmHK3 agenes after 8 days exposure to applied stresses except salinity in leaves, although, their regulation was more prominent during drought stress. Astonishingly, exposure to these stresses showed down-regulation of all genes in maize roots. However, the ZmHK1 behavior was quite different from two other homologues and showed up-regulation in combined stresses. We suggest that ZmHK1 and ZmHK3a, as cytokinin transmembrane receptors, sense osmolarity changes in cells caused by dehydration. Our data supports the involvement of ZmHK homologues under these stresses in maize and provides a gene expression dynamics during the stress which will be valuable for further studies of the molecular mechanisms of stress tolerance in maize.
- Published
- 2013
78. Gene Silencing Method Based on DNA.
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Riasi, Mitra, Karbaschian, Elnaz, and Javadmanesh, Ali
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GENE silencing ,THIOPHOSPHATES ,GENE therapy ,TREATMENT of Duchenne muscular dystrophy ,GENE expression - Abstract
DNA-based approaches can now be utilized as low-risk methods to change gene expression. It appears that this approach has the ability to partially replace RNA-based approaches for altering gene expression, which in the majority of cases leads to immunological responses in patients. When utilized as a technique to silence target gene expression, DNA interference (DNAi) is a single-stranded DNA created to complement the upstream region of a gene. This DNAi molecule is stabilized using a variety of chemical changes, including phosphorothioates, methylphosphonate setC, etc. Several studies of the efficient application of DNA-based methods both in eukaryotic cell lines and the therapy of various disorders, such as Duchenne muscular dystrophy, cancer, etc., have been mentioned. Understanding the DNAi process, its transfer carriers, stabilization techniques, and their limitations is crucial for advancing these applications and predicting the future of DNAi both in basic science and the treatment of disorders brought on by abnormal gene expression. The main purpose of this review is introducing benefits of using DNAi in gene silencing. this review has discussed about different applications of DNAi in drug discovery and treatment, criteria of designing DNAi, possible modifications, introducing different types of carriers and limitations of DNAi administration. [ABSTRACT FROM AUTHOR]
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- 2023
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79. Isolation and culturing myogenic satellite cells from ovine skeletal muscle
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Zahra Rashidian, Nima Dehdilani, Hesam Dehghani, and Ali Javadmanesh
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satellite cells ,sheep ,Veterinary medicine ,myoblasts ,SF600-1100 ,pax7 - Abstract
Sheep satellite cells more than satellite cells of the rat and mouse are similar to human satellite cells. These cells are widely used in the modeling and treatment of diseases like heart insufficiency, neurological diseases, muscular dystrophy, cerebral cell transplantation for the treatment of migraines, screening, and the production of new drugs. This study was aimed to isolate and culture primary satellite cells (PSCs) obtained from sheep fetus, and perform clonal expansion of transfected PSCs. Skeletal muscle tissues of hind limbs were collected from sheep fetuses obtained from a local abattoir. After enzymatic digestion, flasks were replaced after 3 hours to isolate non-myogenic cells, such as fibroblasts. After six days, the cells were differentiated to myoblasts. Using a differentiation medium containing the horse serum, myotube cells were observed in the flask, indicating that the cultured cells were satellite cells. The mRNA expression of the PAX7 gene was used to confirm the presence of satellite cells. In addition, the results showed that satellite cells grow in a culture medium containing 5% FBS without differentiation, while 10% FBS initiates their differentiation.
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- 2020
80. Evaluation of Antimicrobial Activity of Buforin I and Nisin and the Synergistic Effect of Their Combination as a Novel Antimicrobial Preservative
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Farideh Tabatabaei Yazdi, Jebraeil Movaffagh, Ali Javadmanesh, Fakhri Shahidi, and Sahar Roshanak
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0303 health sciences ,Preservative ,biology ,Antimicrobial peptides ,Food spoilage ,04 agricultural and veterinary sciences ,Rhodotorula ,Antimicrobial ,biology.organism_classification ,040401 food science ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,0404 agricultural biotechnology ,chemistry ,Staphylococcus epidermidis ,Listeria ,Food science ,Nisin ,030304 developmental biology ,Food Science - Abstract
One of the most effective methods for increasing the antimicrobial activity of a substance is to combine it with one or more other antimicrobial agents. The aim of the present study was to evaluate the antimicrobial effect of buforin I and nisin alone and investigate the synergistic action of these compounds against the most important food spoilage microorganisms in clouding B. subtilis, S. epidermidis, L. innocua, E. coli, S. Enteritidis, A. oryzae, R. glutinis and G. candidum. The results of MIC and MBC/MFC examinations showed that buforin I had higher antimicrobial activity than nisin on all the microbial strains used in this study (p≤0.5). E.coli was the most resistant to both antimicrobial agents, while Listeria innocua and Staphylococcus epidermidis were the most sensitive to nisin and buforin I, respectively. The results of synergistic interaction between buforin I and nisin indicated that the combination of buforin I and nisin on B. subtilis, S. epidermidis and A. oryzae showed synergistic effect, while it had no effect on S. Enteritidis and Geotrichum candidum. The combination of buforin I and nisin showed partial synergistic effect on Listeria innocua, Escherichia coli, Rhodotorula glutinis. Assessment of viability of the microorganisms under the antimicrobial agents alone and in combination with each other at MICs and FICs indicated that use of these antimicrobial agents in combination enhances antimicrobial activity at lower concentrations of both agents. The present study investigated the antimicrobial properties of buforin I against food spoilage microorganisms for the first time and suggests that its use alone or in combination with nisin may provide a clear horizon for the application of antimicrobial peptides as natural preservatives. Thus, the combination of antimicrobial peptides and traditional antimicrobial food preservative could be a promising option for the prevention of contamination, spoilage, and infestation of food and beverage products.
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- 2020
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81. IgY production in egg yolk against Salmonella typhimurium and salmonella enteritidis
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Shima Eshaghi, Mohammadreza Nassiri, Mojtaba Tahmoorespour, and Ali Javadmanesh
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lcsh:Agriculture ,egg yolk ,lcsh:Biotechnology ,lcsh:TP248.13-248.65 ,embryonic structures ,salmonella ,igy ,lcsh:S ,laying hens - Abstract
Objective Salmonella is a Gram-negative, anaerobic, flagellated bacterium of Salmonella type in Enterobacteriaceae family, which is known as a zoonosis infectious agent. In recent years, different types of antibiotics have been used to overcome the Salmonella infection; however, the increasing number of antibiotic-resistant bacteria, the provision of alternative methods seems be necessary. Specific immunoglobulin Y (IgY) originated from egg yolk causes passive immunity in the fetus, and extracting these antibodies from egg yolk is cheaper and more feasible than other antibodies. Numerous studies have shown that the egg yolk IgY has immunogenic function against a wide range of bacterial and viral infections in mammals. The purpose of this study was to produce specific immunoglobulin Y against Salmonella typhimurium and Salmonella enteritidis bacteria in laying hens. Materials and Methods In the current study, six pullets were inoculated and boosted with one milliliter of killed Salmonella typhimurium and Salmonella enteritidis. Injections were done fortnightly until one week before egg production. After breast muscle injection of chickens, the eggs were collected, and the IgY was extracted from yolk by the Polson method with polyethylene glycol 6000. The produced IgY was approved by SDS-PAGE method. The specific indirect ELISA done by specificity test for purified IgY also approved the specific IgY against both Salmonella typhimurium and Salmonella enteritidis. Results The results of SDS - PAGE demonstrated the presence of two protein bands of 27 and 67 kDa representing light and heavy chains of IgY, respectively. The specific indirect ELISA method proved that the specific IgY against Salmonella typhimurium and Salmonella enteritidis was produced in the egg yolk. Conclusions It might be possible to administer the egg yolk containing specific IgY against both Salmonella typhimurium and Salmonella enteritidis, to induce passive immunity for preventing some pathogenic diseases in calves such as diarrhea.
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- 2020
82. The Comparative Amount of Acrylamide in Tahdig Prepared with the Most Common Edible Liquid and Solid Oils
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Abass Tanhaiean, Marjan Azghandi, Zahra Mousavi, Pushpender Kumar Sharma, Ehab Farag, Maged Argalious, Behrouz Akbari-adergani, Asghar Ahmadi, Gholamreza Jahedkhanki, RaminNabizadeh Nodehi, Jaspreet Kaur Boparai, Narendra Kumar Pandey, Ali Javadmanesh, Dixita Singh, Abhishek Dutt Tripathi , Kundan Singh Adhikari, Parisa Sadighara, Ebtesam Nafie, Islam El-Garawani , Sobhy Hassab El-Nabi, Samraa El-Safey, Mohamed Elfiky, and Veena Paul
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0301 basic medicine ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Nutrition and Dietetics ,030102 biochemistry & molecular biology ,chemistry ,Acrylamide ,Public Health, Environmental and Occupational Health ,Food science ,Food Science - Abstract
Background: Due to the heating of amino acids with edible oils to high temperatures, different amounts of acrylamide are produced. Objective: The purpose of this study was to compare the level of acrylamide in the tahdig of bread and tahdig of potato prepared with the common liquid and solid edible oils, including sunflower, corn, canola, frying oil and solid oils. Methods: The tahdig of bread and potato was prepared under the same temperature and time with different oils. Acrylamide isolation was performed on a solid-phase extraction (SPE) cartridge and acrylamide was determined using High-performance liquid chromatography (HPLC). Results: The highest amount of acrylamide was obtained with sunflower oil in the tahdig of potato (194.091 mg/Kg) and the lowest amount of acrylamide was obtained with solid oil in the tahdig of bread (48.54 mg/Kg). For all the oils, the acrylamide content of the tahdig of potato was higher than bread. Conclusion: This study clearly demonstrated the involvement of the kind of oils in the formation of acrylamide in the tahdig of bread.
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- 2020
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83. In silico study of various antiviral drugs, vitamins, and natural substances as potential binding compounds with SARS-CoV-2 main protease
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Michael Alabboud and Ali Javadmanesh
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covid-19 ,lcsh:Biology (General) ,lcsh:Q ,molecular docking ,mpro ,lcsh:Science ,antiviral ,lcsh:QH301-705.5 - Abstract
The novel coronavirus (SARS-CoV-2) has without a doubt escalated to become a global crisis. Taking into consideration our limited knowledge regarding the virus, all the efforts to provide better understanding or explore the solutions are highly welcomed. In this article, 88 conventional drugs, 16 vitamins, and 63 natural (plant) compounds were chosen to perform a binding simulation with the reported COVID-19 main protease (Mpro) in search for probable inhibitors. Based on docking results, various vitamins (B9, A, K, and E vitamins) exhibited a significantly strong interaction with the studied receptor which might refer to the importance of these supplements in daily diets. Additionally, the strong ligand-protein interactions of some conventional drugs such as Pleconaril, Adefovir dipivoxil, and Stavudine in addition to plant-based compounds such as Curcumin (Curcuma longa), Anolignan A (Anogeissus acuminata), and Phyllamyricin B (Phyllanthus myrtifolius) render these compounds promising and recommended for further studies.
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- 2020
84. Selective capture of plasma cell-free tumor DNA on magnetic beads: a sensitive and versatile tool for liquid biopsy
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Mohammad Amin Kerachian, Ali Javadmanesh, Sina Mozaffari-Jovin, Kamran Ghaffarzadegan, and Marjan Azghandi
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Adult ,Male ,0301 basic medicine ,Cancer Research ,Plasma cell ,medicine.disease_cause ,High Resolution Melt ,Proto-Oncogene Proteins p21(ras) ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Limit of Detection ,Cell Line, Tumor ,medicine ,Humans ,Liquid biopsy ,Aged ,Aged, 80 and over ,Detection limit ,Magnetic Phenomena ,Liquid Biopsy ,DNA, Neoplasm ,General Medicine ,Middle Aged ,Molecular biology ,Microspheres ,030104 developmental biology ,medicine.anatomical_structure ,Oncology ,chemistry ,030220 oncology & carcinogenesis ,Mutation ,Nucleic acid ,Mutation testing ,Molecular Medicine ,Female ,KRAS ,Colorectal Neoplasms ,Cell-Free Nucleic Acids ,DNA - Abstract
Recently, ‘solid tumor biopsies’ have been challenged by the emergence of ‘liquid biopsies’, which are aimed at the isolation and detection of circulating cell-free tumor DNA (ctDNA) in body fluids. Here, we developed and optimized a method for selective capture of ctDNA on magnetic beads (SCC-MAG) for mutation detection in plasma of patients with colorectal cancer (CRC). Blood and tissue samples from 28 CRC patients were included for the detection of KRAS mutations. For the tissue samples, mutation analysis was conducted by high resolution melting (HRM) analysis and sequencing. For the SCC-MAG method, ctDNA was isolated from 200 µl plasma from patients with a mutant KRAS gene. For comparison, ctDNA extraction was carried out using a silica membrane-based method, after which mutations were detected using Intplex allele-specific PCR. The mean ctDNA integrity index in plasma samples of cancer patients was 1.03, comparable with that of silica membrane-derived ctDNA (1.011). Notably, the limit of detection for the SCC-MAG approach was lower than that of the silica membrane method and measured 2.25 pg/ml ctDNA in plasma. Our analyses showed that while the silica membrane-based approach was capable of collecting ctDNA from two out of six CRC patient samples (average Cq 34.23), the SCC-MAG captured ctDNA from all samples with an average Cq of 29.76. We present a robust, reproducible, and highly sensitive method for the analysis of mutation statuses in liquid biopsies. The SCC-MAG method can readily be applied to any nucleic acid target for diagnostic purposes upon careful design of the specific capture probes, and can be multiplexed by several probes to identify multiple targets.
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- 2020
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85. Evaluation of antimicrobial properties of bovine lactoferrin against foodborne pathogenic microorganisms in planktonic and biofilm forms (in vitro)
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Farideh Tabatabaei Yazdi, Zana Pirkhezranian, Ali Javadmanesh, Marjan Azghandi, Sahar Roshanak, and Fakhri Shahidi
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0303 health sciences ,biology ,030306 microbiology ,Chemistry ,Lactoferrin ,Biofilm ,Pathogenic bacteria ,Antimicrobial ,medicine.disease_cause ,biology.organism_classification ,Microbiology ,03 medical and health sciences ,Food Animals ,Listeria monocytogenes ,Staphylococcus aureus ,medicine ,Listeria ,biology.protein ,Agronomy and Crop Science ,Escherichia coli ,030304 developmental biology ,Food Science ,Biotechnology - Abstract
Lactoferrin is one of the most important components in milk. Lactoferrin is an 80 kDa iron-binding glycoprotein that involves a diverse range of biological activities. However, the antimicrobial properties are its most widely studied function. The aim of this study was to assay the antimicrobial and antibiofilm activities of bovine lactoferrin against five of the most important foodborne pathogenic bacterial strains including Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Listeria monocytogenes and Listeria innocua, in planktonic and biofilm forms. Bovine lactoferrin was purchased, MIC and MBC were determined for the mentioned bacterial strains and the effect of lactoferrin concentrations on biofilm formation was evaluated using microtiter plate method. Based on the results, lactoferrin had a greater effect on gram-positive bacteria, L. monocytogenes and L. innocua were the most sensitive strains. MIC for L. monocytogenes, L. innocua, S. aureus and P. aeruginosa was 6, 6, 8 and 14 mg/mL, respectively, Nevertheless, MIC for gram negative E. coli was not observed, even at 16 mg/mL. The result demonstrated that MBC for L. monocytogenes, L. innocua and S. aureus were 10, 12 and 16 mg/mL, respectively. However, MBC for P. aeruginosa and E. coli were not observed for the lactoferrin concentrations evaluated. The highest biofilm formation inhibitory effects of bovine lactoferrin were against L. monocytogenes and L. innocua. To our knowledge, this is the first report on the antibiofilm activity of bovine lactoferrin against foodborne pathogenic bacteria. Our findings suggest lactoferrin to possibly use as an anti-biofilm agent in both food and pharmaceutical industries.
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- 2020
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86. Genetic similarity comparison between some Iranian and Middle Eastern sheep breeds using mitochondrial control region sequencing
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Abdulaziz Hamadalahmad, Mohie Almeziad, and Ali Javadmanesh
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genetic distance ,lcsh:Biology (General) ,mitochondrial genome ,lcsh:Q ,control region ,lcsh:Science ,iranian sheep ,lcsh:QH301-705.5 ,middle east sheep - Abstract
Sheep has been an essential source of food to the inhabitants of the Iranian plateau for centuries. Furthermore, this geographic area is considered the original place of sheep domestication. Phylogenetic studies are highly important in understanding the evolutionary relationships among species. This understanding assists in decision making and planning for genetic resources conservation programs. Analyzing sequences of mitochondrial genome regions provides more reliable evidence regarding the genetic diversity and evolutionary origin of the species, due to the high rate of mitochondrial genome evolution compared to the nucleus. The aim of this study was to use the sequence of mitochondrial control region to investigate the phylogenetic relationship and genetic distances between some domestic sheep breeds of Iran and other Middle Eastern countries. For this purpose, blood samples were collected from Zel, Dalagh, and Mehrabani sheep breeds. After DNA extraction, polymerase chain reaction (PCR) was carried out using specific primers for the targeted mitochondrial genome. Then, PCR products were purified and a standard sequencing was performed. Sequences obtained from this study were compared with other (NCBI) registered sequences of Middle Eastern breeds. Analysis of phylogenetic tree of the main haplotypes of sheep revealed that Zel breed was grouped in the haplotype B with other thin-tailed breeds, such as Karayaka and Sakiz. On the other hand, Mehrabani sheep breed was placed in the haplotype A along with other Middle Eastern fat-tailed breeds such as Naeimi and Saidi. This study provided additional proof for the use of control region sequence as a precise method of genetic distance estimation among sheep breeds.
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- 2020
87. Comparison of Different Signal Sequences to Use for Periplasmic Over-Expression of Buforin I in Escherichia coli: An In Silico Study
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Jebrail Movaffagh, Farideh Tabatabaei Yazdi, Sahar Roshanak, Ali Javadmanesh, and Fakhri Shahidi
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Signal peptide ,Untranslated region ,Exonuclease ,biology ,010405 organic chemistry ,Chemistry ,In silico ,Bioengineering ,Periplasmic space ,medicine.disease_cause ,01 natural sciences ,Biochemistry ,Signal ,0104 chemical sciences ,Analytical Chemistry ,Start codon ,Drug Discovery ,medicine ,biology.protein ,Molecular Medicine ,Escherichia coli - Abstract
Computational prediction of signal peptides is one of the most important steps in genetic engineering experiments. The periplasmic expression cause the reducing in the inherent destructive behavior of Bofurin I against its host and also reducing its susceptibility to proteolytic degradation. In order to predict the best signal peptides for expression of Buforin I in E. coli, 103 signal sequences were retired from signal peptide databases. Since the purpose of this study was to introduce the optimal signal peptides for periplasmic expression, first, sub-cellular localization site of signal peptides was analyzed. Then, n, h, and c regions of signal peptide, signal peptide probability and physico-chemical features were investigated. Base on the results, MalE, hofQ, papK, ugpB, zraP, and sfmC were introduced as the best signal peptides. For increasing the half-life of mRNA and the increasing the stability of the mRNA against exonuclease activity, secondary structures of mRNA including Shine-Dalgarno, untranslated region of ompA, start codon, signal peptide and sequences of Buforin I were analyzed. Based on the total free energy pilot evaluated and mRNA conformations, papK seemed more appropriate than the rest of the signal peptides. The obtained result of this study can be used for design the periplasmic expression constructs.
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- 2020
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88. Intestinal changes and immune responses during Clostridium perfringens-induced necrotic enteritis in broiler chickens
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Ali Daneshmand, Hassan Kermanshahi, Javid Mohammed, Mohammad Hadi Sekhavati, Ali Javadmanesh, Monireh Ahmadian, Marzieh Alizadeh, Jamshid Razmyar, and Raveendra R. Kulkarni
- Subjects
Necrotic enteritis ,Clostridium perfringens ,Immunity ,General Medicine ,histomorphometry ,SF1-1100 ,Enteritis ,immune response ,Diet ,Animal culture ,Necrosis ,broiler chicken ,IMMUNOLOGY, HEALTH AND DISEASE ,Clostridium Infections ,Escherichia coli ,Animals ,Animal Science and Zoology ,Chickens ,Poultry Diseases - Abstract
Clostridium perfringens-induced necrotic enteritis (NE) is an economically important disease of broiler chickens. The present study evaluated the effect of C. perfringens on the intestinal histomorphometry, enteric microbial colonization, and host immune responses using 3 experimental NE reproduction methods. The experimental groups consisted of 1) unchallenged Control diet (corn-soybean meal), 2) Control diet + Eimera inoculation at d 11 followed by C. perfringens challenge at d 15 (ECp), 3) Wheat-based diet + C. perfringens challenge (WCp), and 4) Wheat-based diet + Eimeria inoculation followed by C. perfringens challenge (WECp). The results showed that chickens receiving ECp and WECp had reduced (P < 0.05) bird performance coupled with enteric gross lesions and epithelial damage at d 17 and 24 of age compared to unchallenged control birds. These ECp and WECp administered birds also had increased (P < 0.05) ileal colonization by clostridia and E. coli at d 17 and 24, while the resident Lactobacillus counts were reduced (P < 0.05) at d 24 of age. Furthermore, at d 24, jejunal transcription of IL-6, IL-10, annexin-A1 and IL-2 genes was upregulated (P < 0.05) in the ECp group, whereas the transcription of TNF receptor associated factor (TRAF)-3 gene was increased (P < 0.05) in WECp treated birds when compared to unchallenged control group. Additionally, stimulation of chicken splenocytes and cecal tonsilocytes with virulent C. perfringens bacilli or their secretory proteins resulted in a higher (P < 0.05) frequency of T cells and their upregulation of MHC-II molecule, as determined by flow cytometry. These findings suggest that C. perfringens, while inducing epithelial damage and changes in microbiota, can also trigger host immune responses. Furthermore, NE reproduction methods using coccidia with or without the wheat-based dietary predisposition seem to facilitate an optimal NE reproduction in broiler chickens and thus, may provide better avenues for future C. perfringens research.
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- 2022
89. Improvement of the performance of anticancer peptides using a drug repositioning pipeline
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Mohammadi, Elyas, Tahmoorespur, Mojtaba, Benfeitas, Rui, Altay, Ozlem, Javadmanesh, Ali, Lam, Simon, Mardinoglu, Adil, Sekhavati, Mohammad Hadi, Mohammadi, Elyas, Tahmoorespur, Mojtaba, Benfeitas, Rui, Altay, Ozlem, Javadmanesh, Ali, Lam, Simon, Mardinoglu, Adil, and Sekhavati, Mohammad Hadi
- Abstract
The use of anticancer peptides (ACPs) as an alternative/complementary strategy to conventional chemotherapy treatments has been shown to decrease drug resistance and/or severe side effects. However, the efficacy of the positively-charged ACP is inhibited by elevated levels of negatively-charged cell-surface components which trap the peptides and prevent their contact with the cell membrane. Consequently, this decreases ACP-mediated membrane pore formation and cell lysis. Negatively-charged heparan sulphate (HS) and chondroitin sulphate (CS) have been shown to inhibit the cytotoxic effect of ACPs. In this study, we propose a strategy to promote the broad utilization of ACPs. In this context, we developed a drug repositioning pipeline to analyse transcriptomics data generated for four different cancer cell lines (A549, HEPG2, HT29, and MCF7) treated with hundreds of drugs in the LINCS L1000 project. Based on previous studies identifying genes modulating levels of the glycosaminoglycans (GAGs) HS and CS at the cell surface, our analysis aimed at identifying drugs inhibiting genes correlated with high HS and CS levels. As a result, we identified six chemicals as likely repositionable drugs with the potential to enhance the performance of ACPs. The codes in R and Python programming languages are publicly available in https://github.com/ElyasMo/ACPs_HS_HSPGs_CS. As a conclusion, these six drugs are highlighted as excellent targets for synergistic studies with ACPs aimed at lowering the costs associated with ACP-treatment.
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- 2022
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90. Biodiversity of exopolysaccharide-producing lactic acid bacteria from Iranian traditional Kishk and optimization of EPS yield by Enterococcus spp
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Ferdowsi University of Mashhad, Vosough, Paria Rahnama, Edalatian, Mohammad Reza, Habibi Najafi, Mohammad Bagher, Javadmanesh, Ali, Mayo Pérez, Baltasar, Ferdowsi University of Mashhad, Vosough, Paria Rahnama, Edalatian, Mohammad Reza, Habibi Najafi, Mohammad Bagher, Javadmanesh, Ali, and Mayo Pérez, Baltasar
- Abstract
The production of polysaccharides derived from lactic acid bacteria (LAB) can be a valuable alternative to current polysaccharides. In this study, eight samples of Kishk (traditional dairy product) were collected in sterile conditions and directly cultured on MRS agar medium. Following purification and examination of microscopic, macroscopic characteristics and doing biochemical tests, 143 isolates were selected, and the production of exopolysaccharide (EPS) was investigated by the ruthenium red and disc methods. The EPS production of 79 isolates was confirmed. Total carbohydrate of EPS was determined by the phenol sulfuric acid method. Finally, Enterococcus durans K48, Enterococcus faecium R114, and Enterococcus faecium T52 strains were selected as the best EPS producers. The optimization of EPS production was then performed using Central Composite Design (CCD) and Response Surface Methodology (RSM) approaches. Optimization plots showed the highest EPS yield for E. durans K48, E. faecium R114, and E. faecium T52 occurred at 38.4, 37.4 and 36.7 °C and pH of 5.9, 5.6 and 5.8, respectively, cultured in a Sucrose-MRS medium. Under optimal conditions, the maximum predicted and actual production of EPSs for the examined isolates were 3.18, 3.21, 2.99 and 3.02, 3.15, 3.15, g L, respectively. As determined by Gel Permeation Chromatography, the EPSs molecular weights were in the range of 2.93 × 10 to 3.52 × 10 Da. Analysis of the component monosaccharides by HPLC showed that all three tested EPSs were heteropolysaccharides. After appropriate evaluation, the EPSs produced by native species of LAB isolated from Iranian Kishk could be of interest for industrial applications or as functional food ingredients.
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- 2022
91. Genetic Indications for Anadromous Hilsa Shad (Tenualosa ilisha) in Shatt Al-Arab River Using mtDNA Cytochrome B Gene
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Abdullah, Taqi A., primary, Javadmanesh, Ali, additional, and Al-Noor, Sajed S. H., additional
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- 2022
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92. Identification of lncRNAs expression and their regulatory networks associated with development and growth of skeletal muscle in sheep using RNA-Seq
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Ali Javadmanesh
- Subjects
General Agricultural and Biological Sciences - Published
- 2022
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93. Peripartal Rumen-Protected L-Carnitine Manipulates the Productive and Blood Metabolic Responses in High-Producing Holstein Dairy Cows
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Mohsen Danesh Mesgaran, Hassan Kargar, Sadjad Danesh Mesgaran, and Ali Javadmanesh
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periparturient period ,milk ,General Veterinary ,Veterinary medicine ,SF600-1100 ,L-carnitine ,cow ,food and beverages ,Veterinary Science ,metabolism ,Original Research - Abstract
This study aimed to monitor the effect of including rumen-protected L-carnitine (Carneon 20 Rumin-Pro, Kaesler Nutrition GmbH, Cuxhaven, Germany) in the transition diet on the productive and metabolic responses of multiparous high-producing Holstein dairy cows. Thirty-two multiparous cows were allocated in a completely randomized design to receive the same diet plus 60 g fat prill containing 85% palmitic acid (control, n = 16) or 100 g rumen-protected L-carnitine (RLC, n = 16); at 28 days before expected calving until 28 days in milk (DIM). Fat prill was included in the control diet to balance the palmitic acid content of both experimental diets. Milk production over the 28 DIM for the control and RLC groups was 46.5 and 47.7 kg, respectively. Milk fat content tended to increase upon rumen-protected L-carnitine inclusion (p = 0.1). Cows fed rumen-protected L-carnitine had higher fat- and energy-corrected milk compared with the control group. Pre- and post-partum administration of L-carnitine decreased both high- and low-density lipoprotein concentrations in peripheral blood of post-partum cows. The results of this study indicated that the concentration of triglycerides and beta-hydroxybutyrate was not significantly different between the groups, whereas the blood non-esterified fatty acid concentration was markedly decreased in cows supplemented with L-carnitine. Animals in the RLC group had a significant (p < 0.05) lower blood haptoglobin concentration at 7 and 14 DIM than the control. Animals in the RLC group had a lower concentration of blood enzymes than those of the control group. The mRNA abundance of Toll-like receptors 4, cluster of differentiation 14, and myeloid differential protein 2 did not significantly change upon the supplementation of L-carnitine in the transition diet. In summary, the dietary inclusion of RLC improved dairy cow's performance during the early lactation period. Greater production, at least in part, is driven by improved energy utilization efficiency and enhanced metabolic status in animals during the periparturient period.
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- 2021
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94. Beneficial worm allies warn plants of parasite attack belowground and reduce aboveground 1 herbivore preference and performance 2
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Shokoofeh Kamali, Ali Javadmanesh, Lukasz L Stelinski, Tina Kyndt, Alireza Seifi, Monireh Cheniani, Mohammad Zaki -Aghl, Mojtaba Hosseini, Mahyar Heydarpour, Javad Asili, and Javad Karimi
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- 2021
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95. MS-HRM protocol: a simple and low-cost approach for technical validation of next-generation methylation sequencing data
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Ali Javadmanesh, Afsaneh Mojtabanezhad Shariatpanahi, Ehsan Shams Davodly, Marjan Azghandi, Maryam Yassi, Mehdi Heidari, Matin Kerachian, and Mohammad Amin Kerachian
- Subjects
Genetics ,High-Throughput Nucleotide Sequencing ,General Medicine ,Genomics ,Sequence Analysis, DNA ,DNA Methylation ,Molecular Biology ,Polymerase Chain Reaction - Abstract
DNA methylation is a fundamental epigenetic process and have a critical role in many biological processes. The study of DNA methylation at a large scale of genomic levels is widely conducted by several techniques that are next-generation sequencing (NGS)-based methods. Methylome data revealed by DNA methylation next-generation sequencing (mNGS), should be always verified by another technique which they usually have a high cost. In this study, we offered a low-cost approach to corroborate the mNGS data. In this regard, mNGS was performed on 6 colorectal cancer (case group) and 6 healthy individual colon tissue (control group) samples. An R-script detected differentially methylated regions (DMRs), was further validated by high resolution melting (MS-HRM) analysis. After analyzing the data, the algorithm found 194 DMRs. Two locations with the highest level of methylation difference were verified by MS-HRM, which their results were in accordance with the mNGS. Therefore, in the present study, we suggested MS-HRM as a simple, accurate and low-cost method, useful for confirming methylation sequencing results.
- Published
- 2021
96. Peripartal Rumen-Protected L-Carnitine Manipulates the Productive and Blood Metabolic Responses in High-Producing Holstein Dairy Cows
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Danesh Mesgaran, Mohsen, primary, Kargar, Hassan, additional, Danesh Mesgaran, Sadjad, additional, and Javadmanesh, Ali, additional
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- 2021
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97. Beneficial worm allies warn plants of parasite attack below‐ground and reduce above‐ground herbivore preference and performance
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Kamali, Shokoofeh, primary, Javadmanesh, Ali, additional, Stelinski, Lukasz L., additional, Kyndt, Tina, additional, Seifi, Alireza, additional, Cheniany, Monireh, additional, Zaki‐Aghl, Mohammad, additional, Hosseini, Mojtaba, additional, Heydarpour, Mahyar, additional, Asili, Javad, additional, and Karimi, Javad, additional
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- 2021
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98. Improvement of the performance of anticancer peptides using a drug repositioning pipeline
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Mohammadi, Elyas, primary, Tahmoorespur, Mojtaba, additional, Benfeitas, Rui, additional, Altay, Ozlem, additional, Javadmanesh, Ali, additional, Lam, Simon, additional, Mardinoglu, Adil, additional, and Sekhavati, Mohammad Hadi, additional
- Published
- 2021
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99. Expression of Thanatin in HEK293 Cells and Investigation of its Antibacterial Effects on Some Human Pathogens
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Zahra Mousavi, Ali Javadmanesh, Abbas Tanhaeian, and Marjan Azghandi
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Calcium Phosphates ,0301 basic medicine ,Cell Survival ,medicine.drug_class ,Antimicrobial peptides ,Antibiotics ,Gene Expression ,Peptide ,Microbial Sensitivity Tests ,Transfection ,Biochemistry ,Article ,Microbiology ,Antibiotic resistant ,Mice ,03 medical and health sciences ,Minimum inhibitory concentration ,Structural Biology ,medicine ,Animals ,Humans ,MTT assay ,chemistry.chemical_classification ,Recombinant ,Bacteria ,Base Sequence ,030102 biochemistry & molecular biology ,biology ,Chemistry ,General Medicine ,biology.organism_classification ,Antimicrobial ,Recombinant Proteins ,Anti-Bacterial Agents ,HEK293 Cells ,030104 developmental biology ,NIH 3T3 Cells ,Pathogens ,Antibacterial activity ,Thanatin ,Antimicrobial Cationic Peptides - Abstract
Background:Thanatin is the smallest member of Beta-hairpin class of cationic peptide derived from insects with vast activities against various pathogens.Objective:n this study, the antimicrobial activity of this peptide against some species of human bacterial pathogens as well as its toxicity on NIH cells were evaluated.Method:Thanatin DNA sequence was cloned into pcDNA3.1+ vector and transformed into a DH5α bacterial strain. Then the recombinant plasmids were transfected into HEK-293 cells by calcium phosphate co-precipitation. After applying antibiotic treatment, the supernatant medium containing thanatin was collected. The peptide quantity was estimated by SDS-PAGE and GelQuant software. The antimicrobial activity of this peptide was performed with Minimum Inhibitory Concentration (MIC) method. In addition, its toxicity on NIH cells were evaluated by MTT assay.Results:The peptide quantity was estimated approximately 164.21 µmolL-1. The antibacterial activity of thanatin was estimated between 0.99 and 31.58 µmolL-1 using MIC method. The result of cytotoxicity test on NIH cell line showed that the peptide toxicity up to the concentration of 394.10 µmolL-1 and for 48 hours, was not statistically significant from negative control cells (P>0.05). The antimicrobial assay demonstrated that thanatin had an antibacterial effect on some tested microorganisms. The results obtained in this study also showed that thanatin had no toxicity on mammalian cell lines including HEK293 and NIH.Conclusion:Antimicrobial peptides such as thanatin are considered to be appropriate alternatives to conventional antibiotics in treating various human pathological diseases bacteria.
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- 2019
- Full Text
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100. In Silico Study of Different Signal Peptides to Express Recombinant Glutamate Decarboxylase in the Outer Membrane of Escherichia coli
- Author
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Ali Javadmanesh, Seyed Ali Mortazavi, Masoud Yavarmanesh, and Hanieh Yarabbi
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Signal peptide ,010405 organic chemistry ,Chemistry ,In silico ,Glutamate decarboxylase ,Bioengineering ,Periplasmic space ,01 natural sciences ,Biochemistry ,Protein subcellular localization prediction ,0104 chemical sciences ,Analytical Chemistry ,Secretory protein ,Drug Discovery ,Molecular Medicine ,Bacterial outer membrane ,Secretory pathway - Abstract
Gamma amino butyric acid (GABA) is used as drugs, food ingredients, and dietary supplements. l-glutamate is converted to GABA by the decarboxylation reaction, which is catalyzed by the glutamate decarboxylase (GAD). Escherichia coli is widely being used to express proteins. However, without appropriate signal peptide, it cannot be applied for secretory proteins. Selecting a suitable signal peptide (SP) is a critical step in the secretory production of different proteins. In silico identification of suitable SP is a reliable and cost-effective alternative to experimental approaches. In previous studies, the localization of proteins was not considered and the SPs of periplasmic, membranes and extracellular were compared. Therefore, this study aimed to predict the best SP for the expression of recombinant GAD in the outer membrane of E. coli only. Also, we compared twelve servers to evaluate protein localization, solubility, and secretory pathway. In the present study, 127 SPs were taken from the Signal Peptide database. The localization site, physico-chemical properties, location of cleavage sites, regions and D-score of them were determined by ProtComp, ProtParam, and SignalP 3.0 and 4.1 servers, respectively. To rank SPs based on the secretion properties, PRED-TAT and SignalP 5.0 webservers were used. Based on the results, the localization site of 13 SPs was in the outer membrane of E. coli. Among them, the most suitable candidates seemed to be torT with a reasonably high D-score, aliphatic index, and GRAVY, followed by ccmH and then pspE. TorT accelerates GAD scale-up production and might be useful in future experimental research.
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- 2019
- Full Text
- View/download PDF
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