1
|
Endo S, Sugita T, Kamai S, Nakamura K, Yamazaki F, Sampei S, Snarskis G, Valančiūtė A, Kazemi M, Rokaitis I, Koketsu K. Selective microbial production of lacto-N-fucopentaose I in Escherichia coli using engineered α-1,2-fucosyltransferases. Metab Eng 2024; 82:1-11. [PMID: 38145749 DOI: 10.1016/j.ymben.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/23/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
Lacto-N-fucopentaose I (LNFP I) is the second most abundant fucosylated human milk oligosaccharide (HMO) in breast milk after 2'-fucosyllactose (2'-FL). Studies have reported that LNFP I exhibits antimicrobial activity against group B Streptococcus and antiviral effects against Enterovirus and Norovirus. Microbial production of HMOs by engineered Escherichia coli is an attractive, low-cost process, but few studies have investigated production of long-chain HMOs, including the pentasaccharide LNFP I. LNFP I is synthesized by α1,2-fucosyltransfer reaction to the N-acetylglucosamine moiety of the lacto-N-tetraose skeleton, which is catalyzed by α1,2-fucosyltransferase (α1,2-FucT). However, α1,2-FucTs competitively transfer fucose to lactose, resulting in formation of the byproduct 2'-FL. In this study, we constructed LNFP I-producing strains of E. coli with various α1,2-fucTs, and observed undesired 2'-FL accumulation during fed-batch fermentation, although, in test tube assays, some strains produced LNFP I without 2'-FL. We hypothesized that promiscuous substrate selectivity of α1,2-FucT was responsible for 2'-FL production. Therefore, to decrease the formation of byproduct 2'-FL, we designed 15 variants of FsFucT from Francisella sp. FSC1006 by rational and semi-rational design approaches. Five of these variants of FsFucT surpassed a twofold reduction in 2'-FL production compared with wild-type FsFucT while maintaining comparable levels of LNFP I production. These designs encompassed substitutions in either a loop region of the enzyme (residues 154-171), or in specific residues (Q7, H162, and L164) that influence substrate binding either directly or indirectly. In particular, the E. coli strain that expressed FsFucT_S3 variants, with a substituted loop region (residues 154-171) forming an α-helix structure, achieved an accumulation of 19.6 g/L of LNFP I and 0.04 g/L of 2'-FL, while the E. coli strain expressing the wild-type FsFucT accumulated 12.2 g/L of LNFP I and 5.85 g/L of 2'-FL during Fed-bach fermentation. Therefore, we have successfully demonstrated the selective and efficient production of the pentasaccharide LNFP I without the byproduct 2'-FL by combining protein engineering of α1,2-FucT designed through in silico structural modeling of an α1,2-FucT and docking simulation with various ligands, with metabolic engineering of the host cell.
Collapse
Affiliation(s)
- Shun Endo
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomotoshi Sugita
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Sayaka Kamai
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Kazuki Nakamura
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Fuhito Yamazaki
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Sotaro Sampei
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | | | | | - Masoud Kazemi
- Biomatter, Žirmūnų G. 139A, Vilnius 09120, Lithuania
| | | | - Kento Koketsu
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan.
| |
Collapse
|
2
|
DeAbreu A, Bowness C, Alizadeh A, Chartrand C, Brunelle NA, MacQuarrie ER, Lee-Hone NR, Ruether M, Kazemi M, Kurkjian ATK, Roorda S, Abrosimov NV, Pohl HJ, Thewalt MLW, Higginbottom DB, Simmons S. Waveguide-integrated silicon T centres. Opt Express 2023; 31:15045-15057. [PMID: 37157355 DOI: 10.1364/oe.482008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The performance of modular, networked quantum technologies will be strongly dependent upon the quality of their quantum light-matter interconnects. Solid-state colour centres, and in particular T centres in silicon, offer competitive technological and commercial advantages as the basis for quantum networking technologies and distributed quantum computing. These newly rediscovered silicon defects offer direct telecommunications-band photonic emission, long-lived electron and nuclear spin qubits, and proven native integration into industry-standard, CMOS-compatible, silicon-on-insulator (SOI) photonic chips at scale. Here we demonstrate further levels of integration by characterizing T centre spin ensembles in single-mode waveguides in SOI. In addition to measuring long spin T1 times, we report on the integrated centres' optical properties. We find that the narrow homogeneous linewidth of these waveguide-integrated emitters is already sufficiently low to predict the future success of remote spin-entangling protocols with only modest cavity Purcell enhancements. We show that further improvements may still be possible by measuring nearly lifetime-limited homogeneous linewidths in isotopically pure bulk crystals. In each case the measured linewidths are more than an order of magnitude lower than previously reported and further support the view that high-performance, large-scale distributed quantum technologies based upon T centres in silicon may be attainable in the near term.
Collapse
|
3
|
Roda S, Terholsen H, Meyer JRH, Cañellas-Solé A, Guallar V, Bornscheuer U, Kazemi M. AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design. J Phys Chem B 2023; 127:2661-2670. [PMID: 36944360 PMCID: PMC10068746 DOI: 10.1021/acs.jpcb.2c07091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
With advances in protein structure predictions, the number of available high-quality structures has increased dramatically. In light of these advances, structure-based enzyme engineering is expected to become increasingly important for optimizing biocatalysts for industrial processes. Here, we present AsiteDesign, a Monte Carlo-based protocol for structure-based engineering of active sites. AsiteDesign provides a framework for introducing new catalytic residues in a given binding pocket to either create a new catalytic activity or alter the existing one. AsiteDesign is implemented using pyRosetta and incorporates enhanced sampling techniques to efficiently explore the search space. The protocol was tested by designing an alternative catalytic triad in the active site of Pseudomonas fluorescens esterase (PFE). The designed variant was experimentally verified to be active, demonstrating that AsiteDesign can find alternative catalytic triads. Additionally, the AsiteDesign protocol was employed to enhance the hydrolysis of a bulky chiral substrate (1-phenyl-2-pentyl acetate) by PFE. The experimental verification of the designed variants demonstrated that F158L/F198A and F125A/F158L mutations increased the hydrolysis of 1-phenyl-2-pentyl acetate from 8.9 to 66.7 and 23.4%, respectively, and reversed the enantioselectivity of the enzyme from (R) to (S)-enantiopreference, with 32 and 55% enantiomeric excess (ee), respectively.
Collapse
Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Henrik Terholsen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Jule Ruth Heike Meyer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Albert Cañellas-Solé
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, Barcelona 08010, Spain
| | - Uwe Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
- Biomatter Designs, Žirmu̅n̨ g. 139A, Vilnius 09120, Lithuania
| |
Collapse
|
4
|
Roda S, Fernandez-Lopez L, Benedens M, Bollinger A, Thies S, Schumacher J, Coscolín C, Kazemi M, Santiago G, Gertzen CGW, Gonzalez-Alfonso JL, Plou FJ, Jaeger KE, Smits SHJ, Ferrer M, Guallar V. A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions. Angew Chem Int Ed Engl 2022; 61:e202207344. [PMID: 35734849 PMCID: PMC9540564 DOI: 10.1002/anie.202207344] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 01/01/2023]
Abstract
Engineering dual‐function single polypeptide catalysts with two abiotic or biotic catalytic entities (or combinations of both) supporting cascade reactions is becoming an important area of enzyme engineering and catalysis. Herein we present the development of a PluriZyme, TR2E2, with efficient native transaminase (kcat: 69.49±1.77 min−1) and artificial esterase (kcat: 3908–0.41 min−1) activities integrated into a single scaffold, and evaluate its utility in a cascade reaction. TR2E2 (pHopt: 8.0–9.5; Topt: 60–65 °C) efficiently converts methyl 3‐oxo‐4‐(2,4,5‐trifluorophenyl)butanoate into 3‐(R)‐amino‐4‐(2,4,5‐trifluorophenyl)butanoic acid, a crucial intermediate for the synthesis of antidiabetic drugs. The reaction proceeds through the conversion of the β‐keto ester into the β‐keto acid at the hydrolytic site and subsequently into the β‐amino acid (e.e. >99 %) at the transaminase site. The catalytic power of the TR2E2PluriZyme was proven with a set of β‐keto esters, demonstrating the potential of such designs to address bioinspired cascade reactions.
Collapse
Affiliation(s)
- Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | | | - Marius Benedens
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Alexander Bollinger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Julia Schumacher
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Cristina Coscolín
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Masoud Kazemi
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | - Gerard Santiago
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | - Christoph G W Gertzen
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | | | - Francisco J Plou
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Manuel Ferrer
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| |
Collapse
|
5
|
Aliyari H, Golabi S, Sahraei H, Daliri MR, Minaei-Bidgoli B, Tadayyoni H, Kazemi M. Evaluation of Stress and Cognition Indicators in a Puzzle Game: Neuropsychological, Biochemical and Electrophysiological Approaches. Arch Razi Inst 2022; 77:1397-1403. [PMID: 36883163 PMCID: PMC9985795 DOI: 10.22092/ari.2021.356500.1855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/14/2021] [Indexed: 03/09/2023]
Abstract
Video games have significant and diverse effects on stress and cognitive systems based on the game style. The effect of this media on the central nervous system is significant because of its repetition. Nowadays, video games have become an important part of human life at different ages, and therefore, assessing their effects (good and bad) on stress factors, cognition, and behavior can be an important help in understanding the nature of these games and managing their impact on humans. Consequently, this study aimed to investigate the effect of a puzzle game on the player's stress and cognitive indicators in neuropsychological, biochemical, and electrophysiological approaches. A total of 44 participants were entered into the study and randomly assigned to control and experimental groups. Our interventions were watching (control group) and playing (experimental group) the game. Salivary biomarkers (cortisol and alpha-amylase) were measured using the enzyme-linked immunosorbent assay method. Electrophysiological assessment of attention and stress was performed using electroencephalography. Neuropsychological assessments for the evaluation of mental health, mental fatigue, sustained attention, and reaction time were conducted using paced auditory serial addition test. All tests were administered before and after the interventions. The findings revealed that the salivary cortisol and alpha-amylase significantly reduced after playing the game. There were significantly higher levels of attention after playing the game. Mental health and sustained attention significantly increased after game playing. It can conclude that puzzle-style computer games can strengthen and empower the perceptual-cognitive system and suppress the stress system of players. Therefore, they can be used purposefully as a positive cognitive therapy approach.
Collapse
Affiliation(s)
- H Aliyari
- Center for Human-Engaged Computing, Kochi University of Technology, Kochi, Japan
| | - S Golabi
- Department of Medical Physiology, School of Medicine, Abadan University of Medical Sciences, Abadan, Iran
| | - H Sahraei
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - M R Daliri
- Department of Electrical Engineering, University of Science and Technology, Tehran, Iran
| | - B Minaei-Bidgoli
- School of Computer Engineering, University of Science and Technology, Tehran, Iran
| | - H Tadayyoni
- Department of Electrical and Electronics Engineering, Ozyegin University, Istanbul, Turkey
| | - M Kazemi
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
6
|
Roda S, Fernandez-Lopez L, Benedens M, Bollinger A, Thies S, Schumacher J, Coscolín C, Kazemi M, Santiago G, Gertzen CGW, Gonzalez-Alfonso JL, Plou FJ, Jaeger KE, Smits SHJ, Ferrer M, Guallar V. A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Laura Fernandez-Lopez
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Marius Benedens
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies Wilhelm Johnen Straße, Bldg 15.8, 01/303 40228 Düsseldorf GERMANY
| | - Alexander Bollinger
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Stephan Thies
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Julia Schumacher
- Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies Building 26.44.01.62, Universitaetsstr 1 40228 Düsseldorf GERMANY
| | - Cristina Coscolín
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 28049 Madrid SPAIN
| | - Masoud Kazemi
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Gerard Santiago
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Christoph G. W. Gertzen
- Heinrich Heine University Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Institute for Pharmaceutical and Medicinal Chemistry 40228 Düsseldorf GERMANY
| | - Jose L. Gonzalez-Alfonso
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Francisco J. Plou
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Karl-Erich Jaeger
- Forschungszentrum Julich ICG: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Sander H. J. Smits
- Heinrich Heine University Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies 40228 Düsseldorf GERMANY
| | - Manuel Ferrer
- Institute of Catalysis CSIC Department of Biocatalysis Marie Curie 2Campus Cantoblanco 28049 Madrid SPAIN
| | - Víctor Guallar
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| |
Collapse
|
7
|
Kazemi M, Madani R, Aghamaali MR, Emami T, Golchinfar F, Heshmati L. Preparation and Characterization of Nanoliposome Containing Isolated VP1 Protein of Foot and Mouth Disease Virus as a Model of Vaccine. Arch Razi Inst 2022; 77:37-44. [PMID: 35891774 PMCID: PMC9288613 DOI: 10.22092/ari.2021.353322.1596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/10/2021] [Indexed: 06/15/2023]
Abstract
Foot-and-mouth disease (FMD) is an acute and highly contagious disease in livestock, such as cattle, sheep, and pigs, leading to a lot of economic losses. The current FMD vaccines formulated by inactivated whole-virus and adjuvant successfully reduce disease outbreaks in many regions of the world. Immunological studies on FMD viruses revealed that the dominant epitope in arising neutral antibody response is amino acid residues constructing the G-H loop, constituting a surface loop of the structural protein, termed VP1. Liposomes as one of the most well-known vehicles are considered an important carrier in vaccine development, and their function is used to encapsulate purified VP1 protein based on their size, charge, and lipid content. Accordingly, the VP1 protein was isolated from the FMD virus. This study aimed to compare four methods of VP1 protein encapsulation in the liposome and the extruding effect, as follows: 1) VP1 protein was dissolved in dimethyl sulfoxide and added to the lipid film hydrated by ethanol, 2) the lipid film was hydrated by VP1 protein with 7M urea, 3) the lipid film was hydrated by VP1 protein and freeze-thawed, and 4) the lipid film was hydrated by VP1 protein. The highest encapsulation efficiency was 91% in the second method which purified protein-containing urea. The VP1 protein in the prepared liposome (1, 2-dimyristoyl-sn-glycero-3-phosphocholine: 1, 2-dimyristoyl-sn-glycero-3-phosphocholine: cholesterol) released more than 90% of protein content after 240 h.
Collapse
Affiliation(s)
- M Kazemi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - R Madani
- Department of Pathobiology, Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Department of Proteomics and Biochemistry, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - M R Aghamaali
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - T Emami
- Department of Proteomics and Biochemistry, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - F Golchinfar
- Department of Proteomics and Biochemistry, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - L Heshmati
- Department of Medical Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
8
|
Kazemi M, Aliyari H, Golabi S, Tekieh E, Tavakoli H, Saberi M, Meftahi G, Sahraei H. Improvement of Cognitive Indicators in Male Monkeys Exposed to Extremely Low-Frequency Electromagnetic Fields. Arch Razi Inst 2022; 77:503-511. [PMID: 35891755 PMCID: PMC9288644 DOI: 10.22092/ari.2020.352384.1560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/23/2020] [Indexed: 06/15/2023]
Abstract
Today, the production of extremely low-frequency electromagnetic fields (ELF-EMFs) has significantly increased. This study aimed to investigate the effect of the ELF-EMFs on the structure and function of the brain in male rhesus monkeys in terms of visual learning (VL), visual memory (VM), and visual working memory (VWM). To conduct the study, four monkeys were selected, of whom two monkeys were irradiated by 12-Hz ELF-EMFs with a magnitude of 0.7 microtesla, and two monkeys were tested without irradiation (control group). A blood sample was taken in three stages, namely pre- and post-irradiated and the recovery phases. Changes in the plasma levels of sodium, potassium, and adrenocorticotropic hormone (ACTH) were evaluated. Moreover, gene expression of N-methyl-D-aspartate (NMDA) receptors was assessed. The anatomical change of the brain's prefrontal area was measured by magnetic resonance imaging and Digital Imaging and Communications in Medicine LiteBox file. The abilities of VL, VM, and VWM significantly improved after the irradiation. Furthermore, the expression of the NMDA receptors gene and the plasma levels of sodium, potassium, and ACTH significantly enhanced after the irradiation. However, the prefrontal area was not significantly affected by the irradiation. No significant differences were observed in any of the studied factors in the control group. Our findings suggested that ELF-EMFs irradiation at 12 Hz positively affected VL and VWM. Consequently, 12-Hz ELF-EMFs irradiations can be widely applied to improve cognitive abilities in monkeys.
Collapse
Affiliation(s)
- M Kazemi
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - H Aliyari
- Center for Human-Engaged Computing, Kochi University of Technology, Kochi, Japan
| | - S Golabi
- Department of Medical Physiology, School of Medicine, Abadan University of Medical Sciences, Abadan, Iran
| | - E Tekieh
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - H Tavakoli
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - M Saberi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Gh Meftahi
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - H Sahraei
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
9
|
Kazemi M, Shahsavani D, Arashi M, Rodrigues PC. Estimation in partial linear model with spline modal function. COMMUN STAT-SIMUL C 2021. [DOI: 10.1080/03610918.2019.1622716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- M. Kazemi
- Department of Statistics, Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran
| | - D. Shahsavani
- Department of Statistics, Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran
| | - M. Arashi
- Department of Statistics, Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran
| | - P. C. Rodrigues
- CAST, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| |
Collapse
|
10
|
Heshmati L, Rezayat SM, Madani R, Emami T, Jafari MR, Golchinfar F, Kazemi M, Azimi Dezfouli SM. Immunity Evaluation of an Experimental Designed Nanoliposomal Vaccine Containing FMDV Immunodominant Peptides. Arch Razi Inst 2021; 76:1183-1190. [PMID: 35355777 PMCID: PMC8934104 DOI: 10.22092/ari.2021.352498.1566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/06/2021] [Indexed: 06/14/2023]
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease affecting cloven-hoofed animals. The particular virus causing FMD disease is called FMD virus and is a member of the Aphthovirus genus in the Picornaviridae family. The FMD virus has an 8500 nt long single strain positive RNA genome with one open reading frame (ORF) trapped in an icosahedral capsid protein. This virus genome doesn't have proofreading property which leads to high mutagenesis. It has seven serotypes, including O, A, ASIA, SAT1, SAT2, and C serotypes, as well as many subtypes. Iran is an endemic region for foot-and-mouth disease. Vaccination of susceptible animals with an inactivated whole-virus vaccine is the only way to control the epidemic in many developing countries. Today, conventionally attenuated and killed virus vaccines are being used worldwide. In Iran, animals have been vaccinated every 105 days with an inactivated FMD vaccine. Although commercially available FMD vaccines are effective, they provide short-term immunity requiring regular boosters. A new FMD vaccine is needed to improve immunization, safety, and long-term immune responses. A synthetic peptide vaccine is one of the safe and important vaccines. Peptide vaccine has low immunogenicity, requiring strong adjuvants. Nanoliposomes can be used as new adjuvants to improve immune response. In the current study, nanoliposomal carriers were selected using Dimyristoylphosphatidylcholine (DMPC), dimyristoyl phosphoglycerol (DMPG), and Cholesterol (Chol) as an adjuvant containing two immunodominant synthetic FMDV peptides. The liposomal formulations were characterized by various physicochemical properties. The size, zeta potential, and encapsulation efficiency were optimized, and the obtained nanoliposome was suitable as a vaccine. The efficacy of vaccines has been evaluated in guinea pigs as animal models. Indirect ELISA was used to detect FMDV-specific IgG. The obtained results indicated that although antibody titer was observed, the amount was lower compared to the groups that received inactivated virus-containing liposomes. In addition, the results showed that liposome was an appropriate adjuvant, compared to other adjuvants, such as Alum and Freund, and can act as a depot and induce an immune response.
Collapse
Affiliation(s)
- L Heshmati
- Department of Medical Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - S M Rezayat
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Pharmaceutical Sciences Branch, Islamic Azad University of Tehran, Iran
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Nanotechnology in Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - R Madani
- Department of Pathobiology, Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Department of Proteomics and Biochemistry, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - T Emami
- Department of Proteomics and Biochemistry, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - M R Jafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - F Golchinfar
- Department of Proteomics and Biochemistry, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - M Kazemi
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - S M Azimi Dezfouli
- Department of Foot and Mouth Vaccine Production, Razi Vaccine and Serum Research Institute, Karaj, Iran
| |
Collapse
|
11
|
Ramaswami U, D'Amore S, Finnegan N, Hughes D, Kazemi M. Impact of SARS-CoV-2 (COVID-19) pandemic on patients with lysosomal storage disorders and restoration of services: experience from a specialist centre. Intern Med J 2021; 51:1580-1593. [PMID: 34487419 PMCID: PMC8652804 DOI: 10.1111/imj.15473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 12/01/2022]
Abstract
This study aims to evaluate the impact of the COVID-19 pandemic on the lysosomal disorders unit (LSDU) at Royal Free London NHS Foundation Trust (RFL), a highly specialised national service for diagnosis and management of adults with lysosomal storage disorders (LSD). Review of home care enzyme replacement therapy (ERT) and emergency care, and COVID-19 shielding categories as per UK government guidance. New clinical pathways were developed to manage patients safely during the pandemic; staff well-being initiatives are described. LSDU staff were redeployed and/or had additional roles to support increased needs of hospitalised COVID-19 patients. During the first lockdown in March 2020, 286 of 602 LSD patients were shielding; 72 of 221 had home care ERT infusions interrupted up to 12 weeks. During the pandemic, there was a 3% reduction in home care nursing support required, with patients learning to self-cannulate or require support for cannulation only. There were no increased adverse clinical events during this period. Twenty-one contracted COVID-19 infection, with one hospitalised and no COVID-19 related deaths. In 2020, virtual clinics were increased by 88% (video and/or telephone) compared to 2019. RFL well-being initiatives supported all staff. We provide an overview of the impact of the COVID-19 pandemic on staff and patients attending a highly specialised rare disease service. As far as we are aware, this is the first detailed narrative on the challenges and subsequent rapid adaptations made, both as part of a large organisation and as a specialist centre. Lessons learnt could be translated to other rare disease services and ensure readiness for any future pandemic.
Collapse
Affiliation(s)
- Uma Ramaswami
- Lysosomal Disorders Unit, Royal Free London NHS Foundation Trust, London, UK
| | - Simona D'Amore
- Lysosomal Disorders Unit, Royal Free London NHS Foundation Trust, London, UK
| | - Niamh Finnegan
- Lysosomal Disorders Unit, Royal Free London NHS Foundation Trust, London, UK
| | - Derralynn Hughes
- Lysosomal Disorders Unit, Royal Free London NHS Foundation Trust, London, UK
| | - Masoud Kazemi
- Lysosomal Disorders Unit, Royal Free London NHS Foundation Trust, London, UK
| | | |
Collapse
|
12
|
Kazemi M, Mokhtarpour A. Use of Bentofeed and Persian Melon Peel Biochar in the Decolorization of Water Contaminated with Methylene Blue and their Effects on In vitro Ruminal Fermentation. Arch Razi Inst 2021; 76:335-344. [PMID: 34223732 DOI: 10.22092/ari.2020.126682.1352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/18/2020] [Indexed: 09/30/2022]
Abstract
This study conducted two experiments to evaluate the effects of two cheap adsorbents, including bentofeed (a commercial name of bentonite) and Persian melon peel biochar (PMPB) on the decolorization of water contaminated by methylene blue (MB) and ruminal fermentation pattern. The decolorization efficiency of bentofeed and PMPB at three levels of 0, 4, and 8 mg per 10 ml of 0, 3, 6, and 9 mg/L MB solutions mg/L after 3 and 24 h of incubation was evaluated by its absorbance at 660 nm. At all dye concentrations, PMPB, and bentofeed showed high potential in removing MB from water with an efficiency of 60%-99.5%. In both incubation times, the addition of 8 mg bentofeed had the highest effect on the removal efficiency when the dye concentration was 6 or 9 mg/L. However, the removal efficiency was declined with increasing MB concentration (p <0.05). Experiment two evaluated the effects of various levels (same as experiment one) of MB, bentofeed, and PMPB on in vitro gas production (GP) and volatile fatty acids (VFA) in two individual 4×3 factorial experiments. The potential GP (b), rate constant of gas production (c), metabolizable energy, organic matter digestibility, and total VFA were significantly decreased with increasing MB in the medium (p <0.05), while all parameters were increased when bentofeed or PMPB was added to the medium containing MB (p <0.05). The amounts of acetic, propionic, and butyric acids were not affected by PMPB; however, they changed when bentofeed was added to the medium (p <0.05). The NH3-N concentration was decreased significantly following the increase of MB; moreover, it was increased when PMPB and bentofeed were added to the medium. MB, as a water contaminant agent, had negative effects on ruminal fermentation parameters. Both adsorbents (i.e., PMPB and specially bentofeed) were efficiently able to remove MB from the water. The negative effects of MB on fermentation parameters were also alleviated as a result of using bentofeed or PMPB. It seems that bentofeed has the higher adsorption property of MB, compared to that of the PMPB.
Collapse
Affiliation(s)
- M Kazemi
- Department of Animal Science, Faculty of Agriculture and Animal Science, University of Torbat-e Jam, Torbat-e Jam, Iran.,Department of Animal Science, Faculty of Agriculture and Animal Science, University of Torbat-e Jam, Torbat-e Jam, Iran
| | - A Mokhtarpour
- Research Center of Special Domestic Animals, University of Zabol, Zabol, Iran
| |
Collapse
|
13
|
Abstract
Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.
Collapse
Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| |
Collapse
|
14
|
Kazemi M, Nazari S, Motamed N, Arsang-Jang S, Fallah R. Prediction of Hospitalization Length. Quantile Regression Predicts Hospitalization Length and its Related Factors better than Available Methods. Ann Ig 2021; 33:177-188. [PMID: 33570089 DOI: 10.7416/ai.2021.2423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND Length of hospitalization is one of the most important indices in evaluating the efficiency and effectiveness of hospitals and the optimal use of resources. Identifying these indices' associated factors could be useful. This study aimed to investigate effective factors of the length of hospitalization in Zanjan teaching hospitals in 2018 using the Quantile regression model. METHODS This cross-sectional study was conducted on 1,031 patients. The study population consisted of patients in orthopaedic, pediatric, internal, surgical and intensive care units. The samples were selected by multistage random sampling. The information was collected by a pre-designed checklist. The Quantile regression model and ordinary regression model were performed on the data. RESULTS Of the 1,031 patients admitted to different units, 624 (60.52%) were male. Mean and standard deviation of length of hospitalization for men, women and all patients were 7.25±5.48, 8.09±6.35 and 7.58±5.83 respectively. For 90 percent of patients the length of hospitalization was less than 14 days. Twenty-five percent of patients in pediatric and orthopedic units and ten percent of patients in internal and surgery units were hospitalized less than three days. In all quantiles, patients' length of hospitalization in surgery and orthopedic units, compared to the intensive care unit, and patients hospitalized for injuries and poisonings compared to other causes, had a statistically significant difference. (p<0.05). CONCLUSION Due to the heterogeneity (skewness) of the length of hospital stay in different units of the hospital, the quantile regression model predicts the length of hospital stay more precisely than the ordinary regression models.
Collapse
Affiliation(s)
- M Kazemi
- Department of Biostatistics and Epidemiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - S Nazari
- Department of Biostatistics and Epidemiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - N Motamed
- Department of Health Care Management, Zanjan Social Health Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - S Arsang-Jang
- Department of Biostatistics and Epidemiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - R Fallah
- Department of Biostatistics and Epidemiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| |
Collapse
|
15
|
Kazemi M, Sorzano COS, Carazo JM, Georges AD, Abrishami V, Vargas J. ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions. Prog Biophys Mol Biol 2021; 164:92-100. [PMID: 33450244 DOI: 10.1016/j.pbiomolbio.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 11/27/2022]
Abstract
Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, i.e., the method is restricted to small deformations and cannot determine local patterns of flexibility of small elements, such as secondary structures, which we discuss in the manuscript.
Collapse
Affiliation(s)
- M Kazemi
- Dep. of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049, Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049, Cantoblanco, Madrid, Spain
| | - A des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA; Dept. of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - V Abrishami
- Laboratory of Structural Biology, Helsinki Institute of Life Science HiLIFE, Finland
| | - J Vargas
- Departamento de Optica, Universidad Complutense de Madrid, Avda. Computense s/n, Ciudad Universitaria, 28040, Madrid, Spain; Department of Anatomy and Cell Biology, McGill University, 3640, Rue University, Montréal, QC, H3A 0C7, Canada.
| |
Collapse
|
16
|
Gorji M, Zargar A, Setayeshmehr M, Ghasemi N, Soleimani M, Kazemi M, Hashemibeni B. Releasing and structural/mechanical properties of nano-particle/Punica granatum (Pomegranate) in poly(lactic-co-glycolic) acid/fibrin as nano-composite scaffold. ACTA ACUST UNITED AC 2021; 122:54-64. [PMID: 33393322 DOI: 10.4149/bll_2021_007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effect of poly(lactic‑co‑glycolic acid) (PLGA) on structure, degradation, drug release and mechanical properties of fibrin/pomegranate(F/POM)-based drug‑eluting scaffolds have been studied comprehensively. METHODS AND MATERIAL Nanoparticle-fibrin is prepared from thrombin and fibrinogen dissolved in NaOH and HCl. Then pomegranate powder is added to it. Nanoparticles/pom are provided by freeze drying and freeze milling. The 3-D scaffold of poly(lactide-co‑glycolic acid) (PLGA) was prepared via salt‑leaching solvent/casting leaching method and impregnated with nanofibrin-pom. Structural and chemical component of the scaffolds were evaluated by transmission and scanning electron microscopy and furrier transmission infrared spectroscopy, respectively. Moreover, the scaffolds were characterized from the degradation rate and drug releasing rate points of view of human Adipose Derive Stem Cells (hADSCs). Cytotoxicity effects of the scaffold were evaluated on hADSCs via MTT assay. RESULTS The results showed that the size of nanoparticles was about 100 nm. The scaffold had a slow degradation rate and it caused a sustained release pattern of pom. MTT assay indicated that nanoparticles had no cytotoxicity and fibrin-pom nanoparticles increased compressive strength of PLGA/scaffolds dramatically and also caused a proper compressive modulus. CONCLUSIONS By adding F/POM nanoparticle to PLGA and fabricating a three‑dimensional nanocomposite scaffold (PLGA/F/POM nanoparticle), special physical and mechanical properties also suitable for drug release and cell behavior were achieved, which makes it suitable for cartilage tissue engineering applications (Tab. 1, Fig. 7, Ref. 53) Keywords: hybrid composites, drug delivery, carrier, nanoparticles, scaffold.
Collapse
|
17
|
Kazemi M, Shahsvani D, Arashi M, Rodrigues PC. Identification for partially linear regression model with autoregressive errors. J STAT COMPUT SIM 2020. [DOI: 10.1080/00949655.2020.1857763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- M. Kazemi
- Department of Statistics, Faculty of Mathematical Sciences, University of Guilan, Rasht, Iran
| | - D. Shahsvani
- Department of Statistics, Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran
| | - M. Arashi
- Department of Statistics, Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran
| | - P. C. Rodrigues
- Department of Statistics, Federal University of Bahia, Salvador, Brazil
| |
Collapse
|
18
|
Bani Ali E, Kazemi M, Ali Ghasemzadeh M. A Novel Preparation of Blankophor R Nanoparticles by Reverse Microemulsion Method. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2018.1563553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Elahe Bani Ali
- Department of Chemistry, Qom Branch Islamic Azad University, Qom, I. R. Iran
| | - Masoud Kazemi
- Department of Chemistry, Qom Branch Islamic Azad University, Qom, I. R. Iran
| | | |
Collapse
|
19
|
Jalili C, Kazemi M, Taheri E, Mohammadi H, Boozari B, Hadi A, Moradi S. Exposure to heavy metals and the risk of osteopenia or osteoporosis: a systematic review and meta-analysis. Osteoporos Int 2020; 31:1671-1682. [PMID: 32361950 DOI: 10.1007/s00198-020-05429-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/22/2020] [Indexed: 01/21/2023]
Abstract
The relationship between heavy metal exposure and risk of osteopenia or osteoporosis has biological plausibility, yet it remains inconclusive; therefore, we conducted a systematic review and meta-analysis to evaluate the associations between exposure to heavy metals (i.e., cadmium, lead, and mercury) and the risk of osteopenia or osteoporosis. Databases of MEDLINE, Embase, Scopus, and Web of Science were searched through November 2019, to identify studies that evaluated the relationship between exposure to cadmium, lead, and mercury and risk of osteopenia or osteoporosis in adults. Fourteen eligible studies were included. Effect sizes expressed as pooled odds ratios (OR) and 95% confidence intervals (CI) were estimated using weighted random-effect models. Exposure to cadmium (OR = 1.35; 95% CI: 1.17 to 1.56; P ≤ 0.001) and lead (OR = 1.15; 95% CI: 1.00 to 1.32; P = 0.05) was associated with an increased risk of osteopenia or osteoporosis, unlike mercury. Subgroup analyses showed cadmium exposure increased the risk of osteopenia or osteoporosis in older (> 65 yrs.; OR = 1.43; 95%CI: 1.08 to 1.88, P = 0.01) compared with younger (18-65 yrs.; OR = 1.24; 95% CI: 1.02 to 1.52, P = 0.03) adults. Also, lead exposure increased the risk in men (OR = 1.55; 95% CI: 1.15 to 2.09, P = 0.007) unlike in women. By contrast to urinary levels, blood (OR = 1.26; 95% CI: 1.08 to 1.47, P = 0.003) and dietary (OR = 1.46; 95% CI: 1.28 to 1.67, P < 0.001) levels of cadmium were associated with an increased risk of osteopenia or osteoporosis. Exposure to cadmium and lead may be associated with an increased risk of osteopenia or osteoporosis, although high heterogeneity was detected.
Collapse
Affiliation(s)
- C Jalili
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - M Kazemi
- Division of Nutritional Sciences, Human Metabolic Research Unit, Cornell University, Ithaca, NY, USA
| | - E Taheri
- Environment Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - H Mohammadi
- Department of Clinical Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - B Boozari
- Department of Clinical Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A Hadi
- Halal Research Center of IRI, FDA, Tehran, Iran
| | - S Moradi
- Department of Clinical Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran.
| |
Collapse
|
20
|
Jost E, Kazemi M, Mrkonjić V, Himo F, Winkler CK, Kroutil W. Variants of the Acyltransferase from Mycobacterium smegmatis Enable Enantioselective Acyl Transfer in Water. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02981] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Etta Jost
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Valerija Mrkonjić
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Christoph K. Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
| |
Collapse
|
21
|
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| |
Collapse
|
22
|
Sheng X, Kazemi M, Żądło-Dobrowolska A, Kroutil W, Himo F. Mechanism of Biocatalytic Friedel-Crafts Acylation by Acyltransferase from Pseudomonas protegens. ACS Catal 2020; 10:570-577. [PMID: 31929947 PMCID: PMC6945686 DOI: 10.1021/acscatal.9b04208] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/18/2019] [Indexed: 12/22/2022]
Abstract
![]()
Acyltransferases isolated from Pseudomonas
protegens (PpATase) and Pseudomonas fluorescens (PfATase)
have recently been reported to catalyze
the Friedel–Crafts acylation, providing a biological version
of this classical organic reaction. These enzymes catalyze the cofactor-independent
acylation of monoacetylphloroglucinol (MAPG) to diacetylphloroglucinol
(DAPG) and phloroglucinol (PG) and have been demonstrated to have
a wide substrate scope, making them valuable for potential applications
in biocatalysis. Herein, we present a detailed reaction mechanism
of PpATase on the basis of quantum chemical calculations,
employing a large model of the active site. The proposed mechanism
is consistent with available kinetics, mutagenesis, and structural
data. The roles of various active site residues are analyzed. Very
importantly, the Asp137 residue, located more than 10 Å from
the substrate, is predicted to be the proton source for the protonation
of the substrate in the rate-determining step. This key prediction
is corroborated by site-directed mutagenesis experiments. Based on
the current calculations, the regioselectivity of PpATase and its specificity toward non-natural substrates can be rationalized.
Collapse
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Anna Żądło-Dobrowolska
- Institute of Chemistry, NAWI Graz, BioTechMed Graz, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Wolfgang Kroutil
- Institute of Chemistry, NAWI Graz, BioTechMed Graz, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| |
Collapse
|
23
|
Kazemi M, Sheng X, Himo F. Origins of Enantiopreference of
Mycobacterium smegmatis
Acyl Transferase: A Computational Analysis. Chemistry 2019; 25:11945-11954. [DOI: 10.1002/chem.201902351] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Masoud Kazemi
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| | - Xiang Sheng
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| |
Collapse
|
24
|
Kazemi M, Socan J, Himo F, Åqvist J. Mechanistic alternatives for peptide bond formation on the ribosome. Nucleic Acids Res 2019; 46:5345-5354. [PMID: 29746669 PMCID: PMC6009655 DOI: 10.1093/nar/gky367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/26/2018] [Indexed: 02/04/2023] Open
Abstract
The peptidyl transfer reaction on the large ribosomal subunit depends on the protonation state of the amine nucleophile and exhibits a large kinetic solvent isotope effect (KSIE ∼8). In contrast, the related peptidyl-tRNA hydrolysis reaction involved in termination shows a KSIE of ∼4 and a pH-rate profile indicative of base catalysis. It is, however, unclear why these reactions should proceed with different mechanisms, as the experimental data suggests. One explanation is that two competing mechanisms may be operational in the peptidyl transferase center (PTC). Herein, we explored this possibility by re-examining the previously proposed proton shuttle mechanism and testing the feasibility of general base catalysis also for peptide bond formation. We employed a large cluster model of the active site and different reaction mechanisms were evaluated by density functional theory calculations. In these calculations, the proton shuttle and general base mechanisms both yield activation energies comparable to the experimental values. However, only the proton shuttle mechanism is found to be consistent with the experimentally observed pH-rate profile and the KSIE. This suggests that the PTC promotes the proton shuttle mechanism for peptide bond formation, while prohibiting general base catalysis, although the detailed mechanism by which general base catalysis is excluded remains unclear.
Collapse
Affiliation(s)
- Masoud Kazemi
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden.,Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jaka Socan
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden
| |
Collapse
|
25
|
Amrollahi R, Iraji D, Ghasemi M, Sadeghi H, Kazemi M, Mirzaei H, Rostamifard D, Koohestani S, Mardani M, Shahshenas S, Omrani M, Souri S. Alborz tokamak system engineering and design. Fusion Engineering and Design 2019. [DOI: 10.1016/j.fusengdes.2019.02.111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
26
|
Affiliation(s)
- M. Kazemi
- Department of Statistics, Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran
| | - D. Shahsavani
- Department of Statistics, Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran
| | - M. Arashi
- Department of Statistics, Faculty of Mathematical Sciences, Shahrood University of Technology, Shahrood, Iran
| |
Collapse
|
27
|
Affiliation(s)
- Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691, Stockholm, Sweden
| | - Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691, Stockholm, Sweden
| | - Wolfgang Kroutil
- Department of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691, Stockholm, Sweden
| |
Collapse
|
28
|
Zarandi M, Kazemi M, Mohamadi Z, Ghasemzadeh M. A novel approach to Lithol red nanopigment by water in oil microemulsion method. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.07.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
29
|
Marabini R, Kazemi M, Sorzano COS, Carazo JM. Map challenge: Analysis using a pair comparison method based on Fourier shell correlation. J Struct Biol 2018; 204:527-542. [PMID: 30273658 DOI: 10.1016/j.jsb.2018.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 12/22/2022]
Abstract
This document presents the analysis performed over the Map Challenge dataset using a new algorithm which we refer to as Pair Comparison Method. The new algorithm, which is described in detail in the text, is able to sort reconstructions based on a figure of merit and assigns a level of significance to the sorting. That is, it shows how likely the sorting is due to chance or if it reflects real differences.
Collapse
Affiliation(s)
- R Marabini
- Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
| | - M Kazemi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, The University of Melbourne, VIC 3010, Australia
| | - C O S Sorzano
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| |
Collapse
|
30
|
Abstract
The class I pancreatic elastase from Atlantic salmon is considered to be a cold-adapted enzyme in view of the cold habitat, the reduced thermostability of the enzyme, and the fact that it is faster than its mesophilic porcine counterpart at room temperature. However, no experimental characterization of its catalytic properties at lower temperatures has actually been reported. Here we use extensive computer simulations of its catalytic reaction, at different temperatures and with different peptide substrates, to compare its characteristics with those of porcine pancreatic elastase, with which it shares 67% sequence identity. We find that both enzymes have a preference for smaller aliphatic residues at the P1 position, while the reaction rate with phenylalanine at P1 is predicted to be substantially lower. With the former class of substrates, the calculated reaction rates for salmon enzyme are consistently higher than those of the porcine ortholog at all temperatures examined, and the difference is most pronounced at the lowest temperature. As observed for other cold-adapted enzymes, this is caused by redistribution of the activation free energy in terms of enthalpy and entropy and can be linked to differences in the mobility of surface-exposed loops in the two enzymes. Such mobility changes are found to be reflected by characteristic sequence conservation patterns in psychrophilic and mesophilic species. Hence, calculations of mutations in a single surface loop show that the temperature dependence of the catalytic reaction is altered in a predictable way.
Collapse
Affiliation(s)
- Jaka Sočan
- Department of Cell and Molecular Biology , Uppsala University, Biomedical Center , Box 596 , SE-751 24 Uppsala , Sweden
| | - Masoud Kazemi
- Department of Cell and Molecular Biology , Uppsala University, Biomedical Center , Box 596 , SE-751 24 Uppsala , Sweden
| | - Geir Villy Isaksen
- Department of Cell and Molecular Biology , Uppsala University, Biomedical Center , Box 596 , SE-751 24 Uppsala , Sweden.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , University of Tromsø , N9037 Tromsø , Norway
| | - Bjørn Olav Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , University of Tromsø , N9037 Tromsø , Norway
| | - Johan Åqvist
- Department of Cell and Molecular Biology , Uppsala University, Biomedical Center , Box 596 , SE-751 24 Uppsala , Sweden
| |
Collapse
|
31
|
Kazemi M, Amrollahi R. Simulation, Design, Construction of Duoplasmatron and Diagnostic Neutral Beam System for Alborz Tokamak. J Fusion Energ 2017. [DOI: 10.1007/s10894-017-0148-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
32
|
Roustazade R, Radahmadi M, Yazdani Y, Kazemi M. Therapeutic effects of different doses of saffron extract on memory trend in subchronically stressed rats as determined by behavioral, hormonal, and gene expression assays. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
33
|
Masoudi S, Montazeri SA, Pourdanesh F, Biglarian A, Kazemi M, Rahgozar M. A New Approach to Survival Analysis of Head and Neck Squamous Cell Carcinoma. Arch Iran Med 2017; 20:503-510. [PMID: 28846014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND Squamous cell carcinoma is the most common histological subtype of head and neck cancers. METHODS In a retrospective longitudinal study, we assessed the risk of local or metastatic recurrence and death in 140 patients with head and neck squamous cell carcinoma (HNSCC). Multivariate and shared frailty models were used for survival analysis with sex, primary tumor site, grade and stage of the tumor, and treatment modalities as contributing factors. RESULTS The most frequent site for HNSCC was the oral cavity (30%), followed by the tongue (26.4%). For most primary sites, men were at nearly 2-fold higher risk of local recurrence than women, but there was no difference by sex in the risk of metastatic recurrence. Undifferentiated HNSCC was associated with a higher risk of local recurrence (nearly 4-fold) and metastasis (6-15-fold based on the primary site) than well-differentiated tumors. In early months after surgical resection alone, the risk of local recurrence was higher compared to other treatment modalities. There was a strong dependency between the risk of local and metastatic recurrence. CONCLUSION In conclusion, men diagnosed with HNSCC, those with higher grade or advanced state tumor, and those treated by surgery alone are at higher risk of unfavorable outcomes than others and may need more frequent follow-up visits.
Collapse
Affiliation(s)
- Sahar Masoudi
- Department of Biostatistics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Seyed Ali Montazeri
- Student of Public Health, School of Public Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fereydoun Pourdanesh
- Associate Professor Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Akbar Biglarian
- Assistant Professor of Biostatistics, Department of Biostatistics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Masoud Kazemi
- Assistant Professor Department of Otolaryngology (ENT), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Rahgozar
- Associate Professor of Biostatistics, Department of Biostatistics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| |
Collapse
|
34
|
|
35
|
Abstract
The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed cases where the activation free energy is reduced by around 10 kcal/mol due to entropic effects, corresponding to a rate enhancement of ∼107 compared to the uncatalyzed reaction. However, despite substantial efforts from both the experimental and theoretical side, no real consensus has been reached regarding the origin of such large entropic contributions to enzyme catalysis. Another remarkable instance of entropic effects is found in enzymes that are adapted by evolution to work at low temperatures, near the freezing point of water. These cold-adapted enzymes invariably show a more negative entropy and a lower enthalpy of activation than their mesophilic orthologs, which counteracts the exponential damping of reaction rates at lower temperature. The structural origin of this universal phenomenon has, however, remained elusive. The basic problem with connecting macroscopic thermodynamic quantities, such as activation entropy and enthalpy derived from Arrhenius plots, to the 3D protein structure is that the underlying detailed (microscopic) energetics is essentially inaccessible to experiment. Moreover, attempts to calculate entropy contributions by computer simulations have mostly focused only on substrate entropies, which do not provide the full picture. We have recently devised a new approach for accessing thermodynamic activation parameters of both enzyme and solution reactions from computer simulations, which turns out to be very successful. This method is analogous to the experimental Arrhenius plots and directly evaluates the temperature dependence of calculated reaction free energy profiles. Hence, by extensive molecular dynamics simulations and calculations of up to thousands of independent free energy profiles, we are able to extract activation parameters with sufficient precision for making direct comparisons to experiment. We show here that the agreement with the measured quantities, for both enzyme catalyzed and spontaneous solution reactions, is quite remarkable. Importantly, we can now address some of the most spectacular entropy effects in enzymes and clarify their detailed microscopic origin. Herein, we discuss as examples the conversion of cytidine to uridine catalyzed by cytidine deaminase and reactions taking place on the ribosome, namely, peptide bond formation and GTP hydrolysis by elongation factor Tu. It turns out that the large entropy contributions to catalysis in these cases can now be rationalized by our computational approach. Finally, we address the problem of cold adaptation of enzyme reaction rates and prove by computational experiments that the universal activation enthalpy-entropy phenomenon originates from mechanical properties of the outer protein surface.
Collapse
Affiliation(s)
- Johan Åqvist
- Department
of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Masoud Kazemi
- Department
of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Geir Villy Isaksen
- Department
of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- The
Centre for Theoretical Computational Chemistry, Department of Chemistry, University of Tromsø, N9037 Tromsø, Norway
| | - Bjørn Olav Brandsdal
- The
Centre for Theoretical Computational Chemistry, Department of Chemistry, University of Tromsø, N9037 Tromsø, Norway
| |
Collapse
|
36
|
Nejatbakhsh R, Riyahi S, Farrokhi A, Rostamkhani S, Mahmazi S, Yazdinezhad A, Kazemi M, Shokri S. Ameliorating effects of fennel and cumin extracts on sperm quality and spermatogenic cells apoptosis by inducing weight loss and reducing leptin concentration in diet-induced obese rats. Andrologia 2016; 49. [DOI: 10.1111/and.12748] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2016] [Indexed: 01/22/2023] Open
Affiliation(s)
- R. Nejatbakhsh
- Department of Anatomical Sciences; Faculty of Medicine; Zanjan University of Medical Sciences; Zanjan Iran
| | - S. Riyahi
- Department of Genetics; Faculty of Basic Sciences; Islamic Azad University; Zanjan Branch; Zanjan Iran
| | - A. Farrokhi
- Department of Anatomical Sciences; Faculty of Medicine; Zanjan University of Medical Sciences; Zanjan Iran
| | - S. Rostamkhani
- Department of Genetics; Faculty of Basic Sciences; Islamic Azad University; Zanjan Branch; Zanjan Iran
| | - S. Mahmazi
- Department of Genetics; Faculty of Basic Sciences; Islamic Azad University; Zanjan Branch; Zanjan Iran
| | - A. Yazdinezhad
- Department of Pharmacognosy; Faculty of Pharmacy; Zanjan University of Medical Sciences; Zanjan Iran
| | - M. Kazemi
- Department of Anatomical Sciences; Faculty of Medicine; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - S. Shokri
- Department of Anatomical Sciences; Faculty of Medicine; Zanjan University of Medical Sciences; Zanjan Iran
| |
Collapse
|
37
|
Affiliation(s)
- Masoud Kazemi
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, BMC, SE-751 24 Uppsala, Sweden
| | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Johan Åqvist
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, BMC, SE-751 24 Uppsala, Sweden
| |
Collapse
|
38
|
de la Rosa-Trevín J, Quintana A, del Cano L, Zaldívar A, Foche I, Gutiérrez J, Gómez-Blanco J, Burguet-Castell J, Cuenca-Alba J, Abrishami V, Vargas J, Otón J, Sharov G, Vilas J, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano C, Carazo J. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy. J Struct Biol 2016; 195:93-9. [DOI: 10.1016/j.jsb.2016.04.010] [Citation(s) in RCA: 356] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 12/13/2022]
|
39
|
Nedaeinia R, Sharifi M, Avan A, Kazemi M, Rafiee L, Ghayour-Mobarhan M, Salehi R. Locked nucleic acid anti-miR-21 inhibits cell growth and invasive behaviors of a colorectal adenocarcinoma cell line: LNA-anti-miR as a novel approach. Cancer Gene Ther 2016; 23:246-53. [PMID: 27364574 DOI: 10.1038/cgt.2016.25] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 12/21/2022]
Abstract
Colorectal cancer (CRC) is the third leading cause of cancer-related death and has an extremely poor prognosis. Dysregulation of microRNAs (miRNAs) has been shown to be involved in the pathogenesis and progression of many malignancies. Recent data suggest that microRNA-21 (miR-21) is significantly elevated in different types of cancer, especially colon adenocarcinoma. Against this background, locked nucleic acid (LNA)-modified oligonucleotides have recently been suggested as a novel approach for targeting miRNAs as antisense-based gene silencing. The aim of the current study was to explore the functional role of LNA-anti-miR-21 in a colon adenocarcinoma LS174T cell line. LS174T cells were transfected with LNA-anti-miR-21 for 24, 48 and 72 h. Quantitative real-time reverse transcriptase-PCR (qRT-PCR) was performed to assess miR-21 expression by LNA-anti-miR-21. The viability of the cells was evaluated by MTT (3-[4, 5-dimethylthiazol-2-yl]-2, 5-diphenyl tetrazolium bromide) assay and Annexin V/propidium iodide staining assay was used to detect apoptosis. Moreover, invasive behavior of the cells was evaluated before and after therapy by transwell assay. LNA-anti-miR-21 was successfully transfected in human LS174T cells and suppressed the endogenous miR-21. LNA-anti-miR-21 inhibited the cells' growth followed by induction of apoptosis. LNA-anti-miR-21 (50 pmol/μl) reduced the invasive behaviors of LS174T cells after 24 h, compared with untreated cells and scrambled LNA-transfected cells. However, this effect was more pronounced after 72 h. Our findings suggest the therapeutic potential of LNA-anti-miR-21 in a colon adenocarcinoma for targeting miR-21 expression. Further studies are warranted to investigate the molecular mechanisms underlying this novel inhibitor in colorectal cancer to establish its potential value for treatment of CRC patients with high miR-21 expression.
Collapse
Affiliation(s)
- R Nedaeinia
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Students Research Committee, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - M Sharifi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A Avan
- Molecular Medicine Group, Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - M Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - L Rafiee
- Applied Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - M Ghayour-Mobarhan
- Molecular Medicine Group, Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Biochemistry of Nutrition Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - R Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
40
|
Kazemi M, Habibi M, Amrollahi R. Determination of Average Ion Temperature of the TVD Tokamak by a Simple Charge Exchange Analyzer Detector. J Fusion Energ 2016. [DOI: 10.1007/s10894-016-0102-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
41
|
Eskandari M, Ghalyanchi Langeroudi A, Zeighami H, Rostami A, Kazemi M, Eyni H, Shokri S. Co-administration of ginseng and ciprofloxacin ameliorates epididymo-orchitis induced alterations in sperm quality and spermatogenic cells apoptosis following infection in rats. Andrologia 2016; 49. [DOI: 10.1111/and.12621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- M. Eskandari
- Department of Physiology; Faculty of Medicine; Zanjan University of Medical Sciences; Zanjan Iran
| | - A. Ghalyanchi Langeroudi
- Department of Physiology; Faculty of Medicine; Zanjan University of Medical Sciences; Zanjan Iran
| | - H. Zeighami
- Department of Microbiology; Faculty of Medicine; Zanjan University of Medical Sciences; Zanjan Iran
| | - A. Rostami
- Department of Physiology; Faculty of Medicine; Zanjan University of Medical Sciences; Zanjan Iran
| | - M. Kazemi
- Department of Anatomical Sciences; Faculty of Medicine; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - H. Eyni
- Department of Anatomical Sciences; Faculty of Medicine; Tarbiat Modares University; Tehran Iran
| | - S. Shokri
- Department of Anatomical Sciences; Faculty of Medicine; Zanjan University of Medical Sciences; Zanjan Iran
| |
Collapse
|
42
|
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used for the treatment of pain, fever, inflammation, and some types of cancers. Their mechanism of action is the inhibition of isoforms 1 and 2 of the enzyme cyclooxygenase (COX-1 and COX-2, respectively). However, both nonselective and selective NSAIDs may have side effects that include gastric intestinal bleeding, peptic ulcer formation, kidney problems, and occurrences of myocardial infarction. The search for selective high-affinity COX inhibitors resulted in a number of compounds characterized by a slow, tight-binding inhibition that occurs in a two-step manner. It has been suggested that the final, only very slowly reversible, tight-binding event is the result of conformational changes in the enzyme. However, the nature of these conformational changes has remained elusive. Here we explore the structural determinants of the tight-binding phenomenon in COX-1 with molecular dynamics and free energy simulations. The calculations reveal how different classes of inhibitors affect the equilibrium between two conformational substates of the enzyme in distinctly different ways. The class of tight-binding inhibitors is found to exclusively stabilize an otherwise unfavorable enzyme conformation and bind significantly stronger to this state than to that normally observed in crystal structures. By also computing free energies of binding to the two enzyme conformations for 16 different NSAIDs, we identify an induced-fit mechanism and the key structural features associated with high-affinity tight binding. These results may facilitate the rational development of new COX inhibitors with improved selectivity profiles.
Collapse
Affiliation(s)
- Yasmin Shamsudin
- Department of Cell and Molecular Biology, Uppsala University , Box 596, BMC, SE-751 24 Uppsala, Sweden
| | - Masoud Kazemi
- Department of Cell and Molecular Biology, Uppsala University , Box 596, BMC, SE-751 24 Uppsala, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University , Box 596, BMC, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University , Box 596, BMC, SE-751 24 Uppsala, Sweden
| |
Collapse
|
43
|
Kazemi M. Chemical composition and antimicrobial, antioxidant activities and anti-inflammatory potential of Achillea millefolium L., Anethum graveolens L., and Carum copticum L. essential oils. J Herb Med 2015. [DOI: 10.1016/j.hermed.2015.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
44
|
Kazemi M, Åqvist J. Chemical reaction mechanisms in solution from brute force computational Arrhenius plots. Nat Commun 2015; 6:7293. [PMID: 26028237 PMCID: PMC4458863 DOI: 10.1038/ncomms8293] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/24/2015] [Indexed: 12/23/2022] Open
Abstract
Decomposition of activation free energies of chemical reactions, into enthalpic and entropic components, can provide invaluable signatures of mechanistic pathways both in solution and in enzymes. Owing to the large number of degrees of freedom involved in such condensed-phase reactions, the extensive configurational sampling needed for reliable entropy estimates is still beyond the scope of quantum chemical calculations. Here we show, for the hydrolytic deamination of cytidine and dihydrocytidine in water, how direct computer simulations of the temperature dependence of free energy profiles can be used to extract very accurate thermodynamic activation parameters. The simulations are based on empirical valence bond models, and we demonstrate that the energetics obtained is insensitive to whether these are calibrated by quantum mechanical calculations or experimental data. The thermodynamic activation parameters are in remarkable agreement with experiment results and allow discrimination among alternative mechanisms, as well as rationalization of their different activation enthalpies and entropies. Obtaining activation entropies and enthalpies of a reaction is important for distinguishing between alternative reaction mechanisms. Here the authors use computational methods to accurately obtain the enthalpic/entropic components of the activation free energy for hydrolytic deamination reactions.
Collapse
Affiliation(s)
- Masoud Kazemi
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| |
Collapse
|
45
|
|
46
|
Kazemi M, Biria D, Rismani-Yazdi H. Modelling bio-electrosynthesis in a reverse microbial fuel cell to produce acetate from CO2and H2O. Phys Chem Chem Phys 2015; 17:12561-74. [DOI: 10.1039/c5cp00904a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Bio-electrosynthesis of organic compounds (citrate) in a reverse microbial fuel cell.
Collapse
Affiliation(s)
- M. Kazemi
- Department of Biotechnology
- Faculty of Advanced Sciences and Technologies
- University of Isfahan
- Isfahan
- Iran
| | - D. Biria
- Department of Biotechnology
- Faculty of Advanced Sciences and Technologies
- University of Isfahan
- Isfahan
- Iran
| | | |
Collapse
|
47
|
|
48
|
Abstract
This study reports the chemical composition, antioxidant and anti-inflammatory properties of Anethum graveolens essential oil and its main compounds. The essential oil was obtained from the aerial parts of the plant by hydrodistillation and analysed by using GC/MS. α-Phellandrene (19.12%), limonene (26.34%), dill ether (15.23%), sabinene (11.34%), α-pinene (2%), n-tetracosane (1.54%), neophytadiene (1.43%), n-docosane (1.04), n-tricosane (1%), n-nonadecane (1%), n-eicosane (0.78%), n-heneicosane (0.67%), β-myrcene (0.23%) and α-tujene (0.21%) were found to be the major constituents of the oil. A. graveolens oil exhibit a higher activity in each antioxidant system with a special attention for β-carotene bleaching test (IC50: 15.3 μg/mL) and reducing power (EC50: 11.24 μg/mL). The TLC-bioautography screening and fractionation resulted in the separation of the main antioxidant compounds, which were identified as limonene (45%) and sabinene (32%). The essential oil and its main compounds exhibited a potent NO-scavenging effect and inhibited the expression of inducible NO synthase.
Collapse
Affiliation(s)
- M Kazemi
- a Department of Horticultural Science , Faculty of Agricultural Science and Natural Resources, Science and Research Branch, Islamic Azad University , Tehran , Iran
| |
Collapse
|
49
|
Kazemi M, Li LP. A viscoelastic poromechanical model of the knee joint in large compression. Med Eng Phys 2014; 36:998-1006. [PMID: 24933338 DOI: 10.1016/j.medengphy.2014.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 04/18/2014] [Accepted: 04/26/2014] [Indexed: 10/25/2022]
Abstract
The elastic response of the knee joint in various loading and pathological conditions has been investigated using anatomically accurate geometry. However, it is still challenging to predict the poromechanical response of the knee in realistic loading conditions. In the present study, a viscoelastic, poromechanical model of the knee joint was developed for soft tissues undergoing large deformation. Cartilages and menisci were modeled as fibril-reinforced porous materials and ligaments were considered as fibril-reinforced hyperelastic solids. Quasi-linear viscoelasticty was formulated for the collagen network of these tissues and nearly incompressible Neo-Hookean hyperelasticity was used for the non-fibrillar matrix. The constitutive model was coded with a user defined FORTRAN subroutine, in order to use ABAQUS for the finite element analysis. Creep and stress relaxation were investigated with large compression of the knee in full extension. The contact pressure distributions were found similar in creep and stress relaxation. However, the load transfer in the joint was completely different in these two loading scenarios. During creep, the contact pressure between cartilages decreased but the pressure between cartilage and meniscus increased with time. This led to a gradual transfer of some loading from the central part of cartilages to menisci. During stress relaxation, however, both contact pressures decreased monotonically.
Collapse
Affiliation(s)
- M Kazemi
- Department of Mechanical and Manufacturing Engineering, University of Calgary, 2500 University Drive, N.W., Calgary, Alberta, Canada T2N 1N4
| | - L P Li
- Department of Mechanical and Manufacturing Engineering, University of Calgary, 2500 University Drive, N.W., Calgary, Alberta, Canada T2N 1N4.
| |
Collapse
|
50
|
Shokri S, Kazemi M, Firouzjaei MA, Hemadi M, Moayeri A, Ganjkhani M, Nejatbakhsh R. Melatonin protects testes against lithium-pilocarpine-induced temporal lobe epilepsy in rats: a time course study. Andrologia 2014; 47:343-53. [DOI: 10.1111/and.12269] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2014] [Indexed: 02/04/2023] Open
Affiliation(s)
- S. Shokri
- Department of Anatomy; School of Medicine; Zanjan University of Medical Sciences (ZUMS); Zanjan Iran
| | - M. Kazemi
- Department of Physiology; School of Medicine; ZUMS; Zanjan Iran
| | - M. A. Firouzjaei
- Department of Physiology; School of Medicine; Babol University of Medical Sciences (MUBabol); Babol Iran
| | - M. Hemadi
- Fertility, Infertility and Perinatology Research Center; Imam khomeini Hospital; Faculty of Medicine; Ahvaz Jundishapur University of Medical Sciences (AJUMS); Ahvaz Iran
| | - A. Moayeri
- Department of Anatomy; School of Medicine; Ilam University of Medical Sciences (MedIlam); Ilam Iran
| | - M. Ganjkhani
- Department of Physiology; School of Medicine; ZUMS; Zanjan Iran
| | - R. Nejatbakhsh
- Department of Anatomy; School of Medicine; Zanjan University of Medical Sciences (ZUMS); Zanjan Iran
| |
Collapse
|