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Kargar F, Mortazavi M, Maleki M, Mahani MT, Ghasemi Y, Savardashtaki A. Isolation, Identification and In Silico Study of Native Cellulase Producing Bacteria. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666191127142035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
The purpose of this study was to screen the bacteria producing cellulase enzymes and
their bioinformatics studies.
Background:
Cellulose is a long-chain polymer of glucose that hydrolyzes by cellulases to glucose
molecules. In order to design the new biotechnological applications, some strategies have been used as
increasing the efficiency of enzyme production, generating cost-effective enzymes, producing stable
enzymes and identification of new strains.
Objective:
On the other hand, some bacteria special features have made them suitable candidates for the
identification of the new source of enzymes. In this regard, some native strains of bacteria were screened.
Methods:
These bacteria were grown on a culture containing the liquid M9 media containing CMC to
ensure the synthesis of cellulase. The formation of a clear area in the culture medium indicated decomposition
of cellulose. In the following, the DNA of these bacteria were extracted and their 16S rDNA
genes were amplified.
Result:
The results show that nine samples were able to synthesize cellulase. In following, these strains
were identified using 16S rDNA. The results show that these screened bacteria belonged to the Bacillus
sp., Alcaligenes sp., Alcaligenes sp., and Enterobacter sp.
Conclusion:
The enzyme activity analysis shows that the Bacillus toyonensis, Bacillus sp. strain
XA15-411 Bacillus cereus have produced the maximum yield of cellulases. However, these amounts
of enzyme production in these samples are not proportional to their growth rate. As the bacterial
growth chart within 4 consecutive days shows that the Alcaligenes sp. Bacillus cereus, Bacillus
toyonensis, Bacillus sp. strain XA15-411 have a maximum growth rate. The study of the phylogenetic
tree also shows that Bacillus species are more abundant in the production of cellulase enzyme. These
bioinformatics analyses show that the Bacillus species have different evolutionary relationships and
evolved in different evolutionary time. However, for maximum cellulase production by this bacteria,
some information as optimum temperature, optimum pH, carbon and nitrogen sources are needed for
the ideal formulation of media composition. The cellulase production is closely controlled in microorganisms
and the cellulase yields appear to depend on a variety of factors. However, the further studies
are needed for cloning, purification and application of these new microbial cellulases in the different
commercial fields as in food, detergent, and pharmaceutical, paper, textile industries and also various
chemical industries. However, these novel enzymes can be further engineered through rational design
or using random mutagenesis techniques.
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Affiliation(s)
- Farzane Kargar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Tabriz University of Medical Sciences Tabriz, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mahmood Maleki
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences, Shiraz, Iran
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Beitollahi H, Zaimbashi R, Mahani MT, Tajik S. A label-free aptasensor for highly sensitive detection of homocysteine based on gold nanoparticles. Bioelectrochemistry 2020; 134:107497. [PMID: 32222669 DOI: 10.1016/j.bioelechem.2020.107497] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 11/25/2022]
Abstract
In the present study, an original electrode fabrication approach was devised to create a label free sensitive electrochemical aptasensor for the detection of Homocysteine (Hcy) (Homocysteine signal was used for detection). To bind certain targets, synthetic oligonucleotides used as aptamers (APs) were specifically selected. Aptamers are substitutes for antibodies for analytical devices because of their sensitivity and high affinity. In this study, Hcy-Binding-Aptamer (HBA) was grafted onto the surface of Au nanoparticles/Glassy Carbon Electrode (Au/GCE) in order to create an aptasensor. The effects of buffer concentration, buffer type, interaction time, and aptamer concentration were investigated and optimized. In addition, Differential Pulse Voltammetry (DPV) was implemented to identify homocysteine. Favorable performance was achieved at a detection limit of 0.01 μM (S/N = 3) and linear range 0.05-20.0 μM. Furthermore, the fabricated aptasensor displayed desirable stability and reproducibility. The developed electrochemical aptasensor was found to have reasonable selectivity for the detection of homocysteine in the presence of cysteine and methionine. Analysis of real samples showed good ability of the proposed homocysteine biosensor to provide sensitive, quick, easy, and cost effective measurement of homocysteine in human blood serum and urine samples.
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Affiliation(s)
- Hadi Beitollahi
- Environment Department, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Reza Zaimbashi
- Department of Chemistry, Graduate University of Advanced Technology, Kerman, Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science, High Technology & Environmental Science, Graduate University of Advance Technology, Kerman, Iran
| | - Somayeh Tajik
- Research Center for Tropical and Infectious Diseases, Kerman University of Medical Sciences, Kerman, Iran
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Hoseinzadeh AH, Soorni A, Shoorooei M, Torkzadeh Mahani M, Maali Amiri R, Allahyari H, Mohammadi R. Comparative transcriptome provides molecular insight into defense-associated mechanisms against spider mite in resistant and susceptible common bean cultivars. PLoS One 2020; 15:e0228680. [PMID: 32017794 PMCID: PMC6999899 DOI: 10.1371/journal.pone.0228680] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/20/2020] [Indexed: 01/07/2023] Open
Abstract
Common bean (Phaseolus vulgaris L.) is a major source of proteins and one of the most important edible foods for more than three hundred million people in the world. The common bean plants are frequently attacked by spider mite (Tetranychus urticae Koch), leading to a significant decrease in plant growth and economic performance. The use of resistant cultivars and the identification of the genes involved in plant-mite resistance are practical solutions to this problem. Hence, a comprehensive study of the molecular interactions between resistant and susceptible common bean cultivars and spider mite can shed light into the understanding of mechanisms and biological pathways of resistance. In this study, one resistant (Naz) and one susceptible (Akhtar) cultivars were selected for a transcriptome comparison at different time points (0, 1 and 5 days) after spider mite feeding. The comparison of cultivars in different time points revealed several key genes, which showed a change increase in transcript abundance via spider mite infestation. These included genes involved in flavonoid biosynthesis process; a conserved MYB-bHLH-WD40 (MBW) regulatory complex; transcription factors (TFs) TT2, TT8, TCP, Cys2/His2-type and C2H2-type zinc finger proteins; the ethylene response factors (ERFs) ERF1 and ERF9; genes related to metabolism of auxin and jasmonic acid (JA); pathogenesis-related (PR) proteins and heat shock proteins.
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Affiliation(s)
- Abdul Hadi Hoseinzadeh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Marie Shoorooei
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science, High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Reza Maali Amiri
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Hossein Allahyari
- Department of Plant Protection, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Rahmat Mohammadi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
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Kargar F, Savardashtaki A, Mortazavi M, Mahani MT, Amani AM, Ghasemi Y, Nezafat N. In SilicoStudy of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190401204009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server.Methods:For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina.Results:By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence.Conclusion:By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.
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Affiliation(s)
- Farzane Kargar
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences Shiraz, Iran
| | - Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 71348- 14336, Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies Shiraz University of Medical Sciences Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Razmi ED, Beitollahi H, Mahani MT, Anjomshoa M. TiO2/Fe3O4/Multiwalled Carbon Nanotubes Nanocomposite as Sensing Platform for Simultaneous Determination of Morphine and Diclofenac at a Carbon Paste Electrode. RUSS J ELECTROCHEM+ 2019. [DOI: 10.1134/s1023193518140057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Alijani HQ, Pourseyedi S, Torkzadeh Mahani M, Khatami M. Green synthesis of zinc sulfide (ZnS) nanoparticles using Stevia rebaudiana Bertoni and evaluation of its cytotoxic properties. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.07.103] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Ebrahimipour SY, Mohamadi M, Torkzadeh Mahani M, Simpson J, Mague JT, Sheikhshoaei I. Synthesis and structure elucidation of novel salophen-based dioxo-uranium(VI) complexes: In-vitro and in-silico studies of their DNA/BSA-binding properties and anticancer activity. Eur J Med Chem 2017; 140:172-186. [DOI: 10.1016/j.ejmech.2017.08.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/19/2017] [Accepted: 08/30/2017] [Indexed: 01/11/2023]
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Mortazavi M, Zarenezhad M, Alavian SM, Gholamzadeh S, Malekpour A, Ghorbani M, Torkzadeh Mahani M, Lotfi S, Fakhrzad A. Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus. Hepat Mon 2016; 16:e39196. [PMID: 27882066 PMCID: PMC5111459 DOI: 10.5812/hepatmon.39196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/16/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND The hepatitis C virus (HCV) has six major genotypes. The purpose of this study was to phylogenetically investigate the differences between the genotypes of HCV, and to determine the types of amino acid codon usage in the structure of the virus in order to discover new methods for treatment regimes. METHODS The codon usage of the six genotypes of the HCV nucleotide sequence was investigated through the online application available on the website Gene Infinity. Also, phylogenetic analysis and the evolutionary relationship of HCV genotypes were analyzed with MEGA 7 software. RESULTS The six genotypes of HCV were divided into two groups based on their codon usage properties. In the first group, genotypes 1 and 5 (74.02%), and in the second group, genotypes 2 and 6 (72.43%) were shown to have the most similarity in terms of codon usage. Unlike the results with respect to determining the similarity of codon usage, the phylogenetic analysis showed the closest resemblance and correlation between genotypes 1 and 4. The results also showed that HCV has a GC (guanine-cytosine) abundant genome structure and prefers codons with GC for translation. CONCLUSIONS Genotypes 1 and 4 demonstrated remarkable similarity in terms of genome sequences and proteins, but surprisingly, in terms of the preferred codons for gene expression, they showed the greatest difference. More studies are therefore needed to confirm the results and select the best approach for treatment of these genotypes based on their codon usage properties.
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Affiliation(s)
- Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran
| | - Mohammad Zarenezhad
- Gastroentrohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
- Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Disease, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Saeed Gholamzadeh
- Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran
- Corresponding Authors: Saeed Gholamzadeh, Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran. Tel: +98-7136324100, E-mail: ; Abdorrasoul Malekpour, Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran. Tel: +98-7136324100, E-mail:
| | - Abdorrasoul Malekpour
- Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran
- Corresponding Authors: Saeed Gholamzadeh, Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran. Tel: +98-7136324100, E-mail: ; Abdorrasoul Malekpour, Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran. Tel: +98-7136324100, E-mail:
| | - Mohammad Ghorbani
- Department of Pathology, School of Medicine, Fasa University of Medical Sciences, Fasa, IR Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran
| | - Ali Fakhrzad
- Gastroentrohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
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Yaghoobi MM, Mahani MT. NGF and BDNF expression drop off in neurally differentiated bone marrow stromal stem cells. Brain Res 2008; 1203:26-31. [PMID: 18313646 DOI: 10.1016/j.brainres.2008.01.086] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 12/30/2007] [Accepted: 01/23/2008] [Indexed: 01/01/2023]
Abstract
Bone marrow stromal stem cells (BMSC) express two neurotrophins nerve growth factor (NGF) and brain derived growth factor (BDNF) constitutively and can be differentiated into neuronal-like cells and used to treat neural injuries and diseases. The neurotrophins are required for repair of neural tissues. However, it is not evident whether these cells supply the sufficient amounts of the functional growth factors following neuronal differentiation. This study investigates the expression of NGF, BDNF and their processing enzymes Prohormone convertases (PC) Furin, PC5 and PC6 by Real-time RT-PCR during neural differentiation of rat BMSC. The results showed that all inspected processing enzymes are expressed in the cells. The expression of NGF, BDNF and PC5 decreases following differentiation. In addition, BMSCs express Survivin, an anti-apoptotic gene; however, the differentiated cells reduce its expression similar to two neurotrophins, which could make them susceptible to apoptotic death.
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Affiliation(s)
- Mohammad Mehdi Yaghoobi
- Department of Biotechnology, Research Institute of Environmental Sciences, International Centre for Science, High Technology & Environmental Sciences, Kerman, Iran.
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