Bagher Yakhchali

National Institute of Genetic Engineering and Biotechnology

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Ali Asghar Karkhane

National Institute of Genetic Engineering and Biotechnology

Fatemeh Tabandeh

National Institute of Genetic Engineering and Biotechnology

Hossein Ali Alikhani

University of Tehran

Mahvash Khodabandeh

National Institute of Genetic Engineering and Biotechnology

Seyed Safa-Ali Fatemi

National Institute of Genetic Engineering and Biotechnology

Mohammad Ali Oshaghi

Tehran University of Medical Sciences

Parviz Owlia

Shahed University

Parvin Shariati

National Institute of Genetic Engineering and Biotechnology

Saeed Aminzadeh

National Institute of Genetic Engineering and Biotechnology

Alireza Zomorodipour

National Institute of Genetic Engineering and Biotechnology

Cooperative Institutions

National Institute of Genetic Engineering and Biotechnology

University of Tehran

Tehran University of Medical Sciences

Tarbiat Modares University

Pasteur Institute of Iran

Islamic Azad University, Science and Research Branch

Biotechnology Research Center

Shahid Beheshti University of Medical Sciences

Islamic Azad University, Tehran

Isfahan University of Medical Sciences

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Presence of Eisenia fetida enhanced phytoremediation of anthracene by Lolium perenne

Bioscience Journal (2018)

Akbar Ghavidel Summayah Naji Rad Hossein Ali Alikhani Bagher Yakhchali Ahmad Ali Pourbabai

The efficiency of co-application of Eisenia fetida and ryegrass was evaluated in a process called earthworm-assisted phytoremediation.Anthracene was used as a model compound for polycyclic aromatic hydrocarbons (PAHs).The experiments were conducted on a loamy soil in greenhouse conditions.At the end of the experiment, the soil samples were analyzed for residual anthracene by HPLC.Results showed that, phytoremediation using ryegrass could remove 81% of anthracene; however, the rate of removal was 92% when E. fetida was applied simultaneously.E. fetida alone could also remove the initial concentration of anthracene by 40%.Although ryegrass itself could remove anthracene significantly, the employment of earthworm, together with plant was more efficient than each of them individually.The application of E. fetida could also enhance the growth parameters of ryegrass significantly.In comparison to the control, the presence of E. fetida increased plant dry weight (7.8%), root length (47%), shoots length (32%), and root volume (12%).The number of live earthworms was also increased in the planted pots, indicating the helpfulness of the plant for survival of the earthworm in the PAH-contaminated soil.Although plant and earthworm use completely different mechanisms for anthracene degradation, they improve efficiency and survival of the three-component-system.

Eisenia fetida

10.14393/bj-v34n4a2018-39861

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In silicodesign and construction of metal-binding hybrid proteins for specific removal of cadmium based on CS3 pili display on the surface ofEscherichia coli

Biotechnology and Applied Biochemistry (2013)

Vajiheh Eskandari Bagher Yakhchali Mehdi Sadeghi Ali Asghar Karkhane

In this study, through a combination of bioinformatics and genetic engineering procedures, high-affinity metal-binding peptides were designed and expressed on the surface of Escherichia coli for selective Cd(2+) adsorption. Putative cadmium-binding motifs were identified by searches against the Prosite database and permissive sites in the major subunit (CstH) of the enterotoxigenic E. coli pili were predicted based on the data derived from modeling of 3D structures, secondary structure prediction and assignment, inspection of protein hydropathy and exposed regions, and also protein interaction sites. The metal-binding motifs were inserted into one permissive site of the CstH (amino acid 38) with the aid of the SOEing PCR technique. The capacity and selectivity of the recombinant bacteria displaying hybrid pili to adsorb cadmium were evaluated with the atomic absorption procedure. The levels of Cd(2+) accumulation in the recombinant E. coli strains were 13.9- and 11.33-fold higher than those in the control strain. Cd(2+) was selectively absorbed from a solution containing equal concentrations of four metals, resulting in more than 90% of the total adsorbed metals being Cd(2+) , showing a relatively high affinity for Cd(2+) over other coexisting metal ions.

10.1002/bab.1132

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Bioinformatics analysis of extracellular subtilisin E from Bacillus subtilis

Journal of Biomolecular Structure and Dynamics (2021)

Reza Zolfaghari Emameh Justina Kazokaitė Bagher Yakhchali

Bacillus spp. are the main sources of subtilisin E, which has several applications in biotechnology. The 3D structure of subtilisin E has a significant impact on its efficacy. In this study, we evaluated subtilisin E from Bacillus subtilis subsp. subtilis str. 168 by bioinformatic methods. The results revealed that the subtilisin E sequence from B. subtilis contains highly conserved amino acids, including histidine (H), aspartic acid (D) and serine (S). Subtilisin E cleaves the bonds between hydrophobic and polar amino acids in keratin-associated proteins. The effects of point mutations on the crystal structure of subtilisin E (PDB ID: 1SCJ) showed that changes of asparagine 123 (N123) to valine (V) and serine 331 (S331) to leucine (L) respectively, were the most stabilizing. Genomic analysis of the subtilisin E-coding gene (aprE) indicated that this gene and the yhfN gene are expressed through a σA promoter. The analysis of TBFs revealed AbrB, ScoC, DegU, Hpr, σA, SinR, TenA, and DegU as relevant regulators of aprE expression. Phylogenetic analysis showed that subtilisin Es have highly conserved structures among Bacillus spp., sharing a common ancestor, where their coding genes were duplicated and evolved within the Bacillus spp. As the conclusion, our in silico study demonstrated that the overexpression of the aprE gene and stability of the produced subtilisin E can be improved though system biology methods such as point mutations and identifying the involved transcription factors (TFs) or/and TBFs.Communicated by Ramaswamy H. Sarma

Subtilisin

10.1080/07391102.2021.1894979

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Malpighian tubules are important determinants of Pseudomonas transstadial transmission and longtime persistence in Anopheles stephensi

Parasites & Vectors (2015)

Ali Reza Chavshin Mohammad Ali Oshaghi Hassan Vatandoost Bagher Yakhchali Fahimeh Zarenejad

Pseudomonas is a genus of bacteria commonly found in investigations of gut microbes in malaria mosquitoes. Among those mosquitoes is the dominating malaria vector in Asia, Anopheles stephensi, where Pseudomonas is a prevailing bacterium and natural inhabitant of its breeding places. In order to explore the reason for finding Pseudomonas so frequently, an investigation of its localization and transstadial properties was undertaken.A Pseudomonas isolate from An. stephensi was transformed successfully with an endogenous plasmid modified to express green fluorescent protein (GFP). Subsequently, the Pseudomonas-GFP was added to the laboratory larval breeding place of An. stephensi and taken up by the larvae. After 24 hours, the larvae were cleaned and moved to a bath with double-distilled water. Also, female adults were fed sugar solution containing Pseudomonas-GFP. The Pseudomonas-GFP was traced in the alimentary canal of larvae, pupae and adults.Fluorescent microscopy and PCR assays showed that the Pseudomonas bacteria underwent transstadial transmission from larvae to pupae and then to adults. In blood-fed female mosquitoes, the bacteria increased in numbers and remained in the mosquito body for at least three weeks after eclosion. In addition to the midgut, the Malpighian tubules of both larvae and adult mosquitoes were colonized by the bacteria. Also Pseudomonas-GFP that was distributed through sugar solution was able to colonize the Malpighian tubules of adult females.Colonization of the Malpighian tubules by Pseudomonas bacteria seems to be important for the transstadial passage from larvae to adult and presumably for the longevity of the bacteria in the adult mosquito. The existence of an entry point in the larval stage, and the long duration in the female gut, opens up for a possible use of Pseudomonas in mosquito paratransgenesis.

Anopheles stephensi

Malpighian tubule system

Hemolymph

Anopheles culicifacies

10.1186/s13071-015-0635-6

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Citations (79)

Evaluation of nine popular de novo assemblers in microbial genome assembly

Journal of Microbiological Methods (2017)

Esmaeil Forouzan Masoumeh Sadat Mousavi Maleki Ali Asghar Karkhane Bagher Yakhchali

Sequence assembly

10.1016/j.mimet.2017.09.008

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Citations (15)

Cloning and Expression of an Indigenous Mesophile lipase and Evaluation of Bacillus Codon Translation in Pichia Pastoris under Control of Two Different Promoters

Journal of Applied Biotechnology Reports (2016)

Fathollah Ahmadpour Bagher Yakhchali Seyed Safa Ali Fatemi Ali Asghar Karkhane Samira Talebi

Lipases are versatile biocatalysts with a wide range of application in food, dairy, leather, paper, pharmaceutical and detergent industries. In this study, mesophilic lipase gene from an indigenous Bacillus pumilus F3 that already its gene had been sequenced and identified, was cloned and expressed in methylotrophic yeast Pichia pastoris and codon translation of lipase gene was evaluated in P. pastoris under control of‌ two different promoters (alcohol oxidase (AOX1) and glyceraldehid phosphate dehydrogenase(GAPDH) promoters). In addition, the expression conditions of recombinant lipase F3 was optimized in P. pastoris expression system using BMMY medium at pH=3 ,26oC in 0.75% methanol. The lipase gene of 648bp with natural signal peptid sequence from B. pumilus F3 and the codon optimized lipase gene cloned and expressed in methylotrophic yeast P. pastoris. The lipase gene was excised from the recombinant plasmid with BamHI, EcoRI enzymes and ligated to the pPIC9 and pGAP9 linearized with the same enzymes. The recombinant plasmids were confirmed by the PCR and restriction enzyme digestion. The Bgl II linearized Ppic9 and pGAP9 recombinant plasmids were introduced into the yeast P. pastoris GS115 genom by electroporation and confirmed by PCR. Lipase expressing yeast was cultivated in a 250-ml shaking flask containing medium expression. Expression of lipase gene was confirmed using p-nitrophenyl palmitate test and SDS-PAGE. Codon optimized lipase produced as well as native gene and lipase expression was low in both. Also, these results suggest that protein structure is more important than codon preference in expression of proteins such as lipases.

Bacillus pumilus

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Plant Growth Promoting Characterization of Indigenous Azotobacteria Isolated from Soils in Iran

Current Microbiology (2012)

Davoud Farajzadeh Bagher Yakhchali Nasser Aliasgharzad Nemat Sokhandan-Bashir Malak Farajzadeh

Chitinase

Azotobacter

Azotobacter vinelandii

Azotobacter chroococcum

10.1007/s00284-012-0083-x

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Drug Susceptibility and Molecular Epidemiology of Pseudomonas aeruginosa Isolated in a Burn Unit

American Journal of Infectious Diseases (2009)

Hassan Salimi Parviz Owlia Bagher Yakhchali Abdolaziz Rastegar L

Problem statement: Pseudomonas aeruginosa is an opportunistic pathogen that still develops life-threatening infections in patients with immunological system defects, like burn patients, especially in developing countries. Since this bacterium is naturally resistant to many drugs and is able to get resistance to all effective antibiotics, the infection with this organism is particularly problematic condition for patients. This study was design to evaluated drug susceptibility for determination of multidrug-resistant isolates and molecular epidemiology of P. aeruginosa colonization for investigation of the isolates routes in the burn unit of Shahid Motahhari Hospital in Tehran. Approach: About 127 clinical and 2 environmental P. aeruginosa isolates were collected during 6 months. All P. aeruginosa isolates were analyzed for drug susceptibility by disk diffusion method and molecular epidemiology assessment were done by RAPD-PCR analysis. Results: Drug susceptibility tests were shown high resistance for ceftizoxime (86.8%), aztreonam (80.6%), kanamycin (79.8%) and tetracycline (78.3%); furthermore, low resistance for some antibiotics like imipenem (30.2%), piperacillin/tazobactam (34.1%) and amikacin (41.1%) was showed. In addition, 42 multidrug-resistant P. aeruginosa isolates were recovered from clinical specimens and one isolate from environmental samples. Molecular typing revealed eight different profiles that include two profiles, RAPD1 and RAPD4, with environmental resource. The major RAPD profile was RAPD1 profile (n = 64, 50.4%), which includes 31 (72.1%) multidrug-resistant isolates with an environmental reservoir. Conclusion: In summery, we were found three different profiles for multidrug-resistant strains. Different RAPD profiles suggested the different resources of infection, two environmental resources were found, that one of them was multidrug-resistant strain. These findings highlighted the need for further attention to disinfection inanimate hospital environment and controlled contact between staff with patients to limit transfer of P. aeruginosa in this BU; moreover, use of some antimicrobial agents must be restricted due to existence of high resistance and using of combined effective antibiotics is recommend.

10.3844/ajidsp.2009.301.306

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Isolation and Identification of a New Bacillus cereus Strain and Characterization of its Neopullulanase

Applied food biotechnology (2015)

Soheila Davaeifar Parvin Shariati Fatemeh Tabandeh Bagher Yakhchali

Article Info Identification and use of more efficient enzymes in the food and pharmaceutical industries is the focus of many researchers. The aim of this study was to search for a new bacterial strain capable of producing high levels of pullulanase applicable to biotechnology, the starch bioprocessing and food industries. A new pullulan hydrolyzing Bacillus strain was isolated and designated SDK2. Morphological and biochemical tests identified the strain as a putative Bacillus cereus strain, which was further characterized and confirmed through 16s rRNA sequencing, and was submitted to GeneBank, under the accession number FR6864500. Quantitative analysis of the strain’s pullulanase activity was carried out by the Dintrosalicyclic (DNS) acid-based assay. Thin layer chromatography (TLC) of the culture supernatant, identified the extracellular pullulanase as neopullulanase. Effects of temperature and pH on pullulanase activity were also studied. The optimum conditions for enzyme activity, as represented by 60 ° C and a pH of 7, resulted in an activity of 13.43 U/ml, which is much higher than some of the previously reported activities. However, growth of B. cereus SDK2 was also observed at a pH range of 5 to 10, and temperatures of 30 ° C to 50 ° C. The effect of metal ions and reagents, such as Mg +2 , Ca +2 , Zn +2 , Cu +2 , Fe +2 , Ni +2 on enzyme activity showed that Ca +2 ions increased pullulan activity, whereas the other ions and reagents inhibited pullulanase activity. The ability of B. cereus SDK2 to produce high levels of neopullulanase stable at 60

Pullulanase

Pullulan

Strain (injury)

Cereus

10.22037/afb.v2i2.8151

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CLONING, EXPRESSION AND PURIFICATION OF MUTATED FORM OF GEOBACILLUS THERMOCATENULATUS LIPASE IN PICHIA PASTORIS

Ghafoori Ali Asghar Karkhane Mahmoud Azimi Bagher Yakhchali Mehdi Shamsara

Cloning (programming)

Pichia

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