Search for: gene-sequence
Biodegradation of cyanide under alkaline conditions by a strain of pseudomonas putida isolated from gold mine soil and optimization of process variables through response surface methodology (RSM), Article Periodica Polytechnica Chemical Engineering ; Volume 62, Issue 3 , May , 2018 , Pages 265-273 ; 03245853 (ISSN) ; Yaghmaei, S ; Ghobadi Nejad, Z ; Sharif University of Technology
Budapest University of Technology and Economics 2018
In regard to highly poisonous effects of cyanide ion, concerns have been focused recently on treatment of such compounds in different ways. Four bacterial strains (C1-C4) capable of using cyanide as nitrogen source were isolated from contaminated gold mine soil samples under alkaline conditions at 30 °C, pH 9.5-10.5, and agitation speed 150 rpm. The gram-negative bacterium C3 (identified as Pseudomonas parafulva NBRC 16636(T) by 16S rRNA gene sequencing) was able to tolerate cyanide up to 500 ppm besides removing 93.5% of 200 ppm cyanide in 13 days which was confirmed by microorganisms growth. The addition of basal salts enhanced the removal efficiency of C3 by 16%. Cyanide removal...
Article Medical Hypotheses ; Volume 144 , 2020 ; Rabiee, M ; Bagherzadeh, M ; Rezaei, N ; Sharif University of Technology
Churchill Livingstone 2020
Humanity's challenges are becoming increasingly difficult, and as these challenges become more advanced, the need for effective and intelligent action becomes more apparent. Meanwhile, the novel coronavirus disease (COVID-19) pandemic, which has plagued the world, could be considered as an opportunity to take a step toward the need for atomic engineering, compared to molecular engineering, as well as to accelerate this type of research. This approach, which can be expressed in terms of picotechnology, makes it possible to identify living cell types or in general, chemical and biological surfaces using their atomic arrays, and applied for early diagnosis even treatment of the disease. © 2020...
The identification and performance assessment of dominant bacterial species during linear alkylbenzene sulfonate (LAS)-biodegradation in a bioelectrochemical system, Article Bioprocess and Biosystems Engineering ; Volume 44, Issue 12 , 2021 , Pages 2579-2590 ; 16157591 (ISSN) ; Vahabzadeh, F ; Mardanpour, M. M ; Sharif University of Technology
Springer Science and Business Media Deutschland GmbH 2021
The anionic surfactant linear alkylbenzene sulfonate (LAS) is a major chemical constituent of detergent formulation. Regarding the recalcitrant nature of sulfonoaromatic compounds, discharging these substances into wastewater collection systems is a real environmental issue. A study on LAS biodegradation based on bioelectrochemical treatment and in the form of developing a single-chamber microbial fuel cell with air cathode is reported in the present work. Pretreatment study showed LAS concentration of 60 ppm resulted in the highest anaerobic LAS removal of 57%; so, this concentration was chosen to run the MFC. After the sustained anodic biofilm was formed, LAS degradation rate during 4 days...
Study potential of indigenous pseudomonas aeruginosa and bacillus subtilis in bioremediation of diesel-contaminated water, Article Water, Air, and Soil Pollution ; Volume 228, Issue 1 , 2017 ; 00496979 (ISSN) ; Kariminia, H. R ; Ghobadi Nejad, Z ; Fletcher, T. H ; Sharif University of Technology
Petroleum products which are used in a wide variety of industries as energy sources and raw materials have become a major concern in pollution of terrestrial and marine environments. The purpose of this study was to assess the potential of indigenous microbial isolates for degradation of diesel fuel. Two most proficient bacterial strains among five isolated strains from polluted soil of an industrial refinery were studied. The isolates then were identified as Pseudomonas aeruginosa and Bacillus subtilis using biochemical tests and 16S rRNA gene sequence analyses. P. aeruginosa showed higher biodegradation efficiency than B. subtilis in shaking flask containing diesel-contaminated water. P....
Article International Journal of Environmental Science and Technology ; Volume 17, Issue 1 , April , 2020 , Pages 143-152 ; Mahmoodi, R ; Mollania, N ; Kheirabadi, M ; Sharif University of Technology
Environmental pollutions with heavy metals pose serious health and ecological risks. Sabzevar in the northeast of Iran has natural chromic mines and then chromium-polluted soils and groundwater. In the present work, the metal-tolerant bacterial strain KR2 was identified as Shewanella sp. following 16S rDNA gene sequence analysis. Bioremediation ability of isolated bacterial from agricultural soils that irrigated by groundwater, Shewanella sp., was evaluated for uptaking of chromium with varying Cr(VI) concentrations from 50 to 500 ppm in aerobic conditions (pH 7.0, 37 °C). The Shewanella sp. strain KR2 showed an obvious heavy metal tolerant in the wide range of heavy metals including: Cr6+,...
The performances of the chi-square test and complexity measures for signal recognition in biological sequences, Article Journal of Theoretical Biology ; Volume 251, Issue 2 , 2008 , Pages 380-387 ; 00225193 (ISSN) ; Kargar, M ; Sheari, A ; Poormohammadi, H ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Sharif University of Technology
With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the...
Article Nanomedicine ; Volume 16, Issue 3 , 2021 , Pages 237-258 ; 17435889 (ISSN) ; Ahmadi, S ; Fatahi, Y ; Rabiee, M ; Bagherzadeh, M ; Dinarvand, R ; Bagheri, B ; Zarrintaj, P ; Saeb, M. R ; Webster, T. J ; Sharif University of Technology
Future Medicine Ltd 2021
With significant advancements in research technologies, and an increasing global population, microfluidic and nanofluidic systems (such as point-of-care, lab-on-a-chip, organ-on-a-chip, etc) have started to revolutionize medicine. Devices that combine micron and nanotechnologies have increased sensitivity, precision and versatility for numerous medical applications. However, while there has been extensive research on microfluidic and nanofluidic systems, very few have experienced wide-spread commercialization which is puzzling and deserves our collective attention. For the above reasons, in this article, we review research advances that combine micro and nanotechnologies to create the next...
Efficient biodegradation of naphthalene by a newly characterized indigenous achromobacter sp. FBHYA2 isolated from Tehran oil refinery complex, Article Water Science and Technology ; Volume 66, Issue 3 , March , 2012 , Pages 594-602 ; 02731223 (ISSN) ; Borghei, S. M ; Hassani, A. H ; Yakhchali, B ; Ardjmand, M ; Zeinali, M ; Sharif University of Technology
IWA Pub 2012
A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30°C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals...
Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil, Article Functional and Integrative Genomics ; Volume 18, Issue 5 , 2018 , Pages 533-543 ; 1438793X (ISSN) ; Niazi, A ; Deihimi, T ; Taghavi, S. M ; Ayatollahi, S ; Ebrahimie, E ; Sharif University of Technology
Springer Verlag 2018
One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison...
An efficient biosurfactant-producing bacterium pseudomonas aeruginosa MR01, isolated from oil excavation areas in south of Iran, Article Colloids and Surfaces B: Biointerfaces ; Volume 69, Issue 2 , 2009 , Pages 183-193 ; 09277765 (ISSN) ; Shourian, M ; Roostaazad, R ; Rouholamini Najafabadi, A ; Adelzadeh, M. R ; Akbari Noghabi, K ; Sharif University of Technology
A bacterial strain was isolated and cultured from the oil excavation areas in tropical zone in southern Iran. It was affiliated with Pseudomonas. The biochemical characteristics and partial sequenced 16S rRNA gene of isolate, MR01, was identical to those of cultured representatives of the species Pseudomonas aeruginosa. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties. Compositional analysis revealed that the extracted biosurfactant was composed of high percentages lipid (∼65%, w/w) and carbohydrate (∼30%, w/w) in addition to a minor fraction of protein (∼4%, w/w). The best production of 2.1 g/l was obtained when the cells were grown on...
Point-of-use rapid detection of sars-cov-2: Nanotechnology-enabled solutions for the covid-19 pandemic, Article International Journal of Molecular Sciences ; Volume 21, Issue 14 , 2020 , Pages 1-23 ; Bagherzadeh, M ; Ghasemi, A ; Zare, H ; Ahmadi, S ; Fatahi, Y ; Dinarvand, R ; Rabiee, M ; Ramakrishna, S ; Shokouhimehr, M ; Varma, R. S ; Sharif University of Technology
MDPI AG 2020
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is yet available as a treatment. Considering the global healthcare urgency, several techniques, including whole genome sequencing and computed tomography imaging have been employed for diagnosing infected people. Considerable efforts are also directed at detecting and preventing different modes of community transmission. Among them is the rapid detection of virus presence on different surfaces with which people may come in...