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Article ; Online: Theoretical study of RNA-polymerase behavior considering the backtracking state.

Kor, Razieh / Mohammad-Rafiee, Farshid

2022 Volume 18, Issue 32, Page(s) 5979–5988

Abstract: The dynamical behavior of the RNA polymerase in the transcription process is vital to gene expression. During the transcription process, the 3' end of the transcribed RNA can be dislocated from the active site of the enzyme and as a result, the RNA ... ...

Abstract	The dynamical behavior of the RNA polymerase in the transcription process is vital to gene expression. During the transcription process, the 3' end of the transcribed RNA can be dislocated from the active site of the enzyme and as a result, the RNA polymerase goes to the backtracked state. Here, we develop a theoretical model to study the transcription process considering the backtracking state. We aim at describing the behavior of the enzyme in the backtracking state in the presence of an external force, which leads to two possibilities: (i) rescuing from the backtracking state and, (ii) the arresting of the enzyme. We study the probability and the rate of the mentioned processes. In addition, we find that entering the backtracking state behaves like the Brownian ratchet mechanism. This model could shed some light on the modeling of the transcription process and further studies on the energy landscape of the backtracking channel and the gene regulation.
MeSH term(s)	Catalytic Domain ; DNA-Directed RNA Polymerases/chemistry ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Models, Theoretical ; RNA/chemistry ; Transcription, Genetic
Chemical Substances	RNA (63231-63-0) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2022-08-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d2sm00232a
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Photodynamic Therapy and Its Synergism with Melittin Against Drug-Resistant Acinetobacter baumannii Isolates with High Biofilm Formation Ability.

Babaeekhou, Laleh / Ghane, Maryam / Mohammad Rafiee, Masoumeh

Current microbiology

2023 Volume 80, Issue 10, Page(s) 324

Abstract: Drug-resistant biofilm producer A. baumannii isolates are a global concern that warns researchers about the development of new treatments. This study was designed to analyze the effect of photodynamic therapy (PDT) as monotherapy and associated with ... ...

Abstract	Drug-resistant biofilm producer A. baumannii isolates are a global concern that warns researchers about the development of new treatments. This study was designed to analyze the effect of photodynamic therapy (PDT) as monotherapy and associated with melittin on multidrug-resistant A. baumannii isolates. Sub-lethal doses of photosensitizer, LED, and PDT were determined. The PDT effect on the biofilm and expression of biofilm-associated genes was evaluated by scanning electron microscopy and quantitative real-time PCR (qRT-PCR) methods, respectively. The synergistic effect of PDT and melittin on the survival of MDR/XDR strong biofilm producer isolates was evaluated by checkerboard assay. Survival rates were significantly decreased at the lowest concentration of 12.5-50 μg/ml in 4 min at an energy density of 93.75 J/cm
MeSH term(s)	Melitten/pharmacology ; Acinetobacter baumannii/genetics ; Anti-Bacterial Agents/pharmacology ; Biofilms ; Photochemotherapy
Chemical Substances	Melitten (20449-79-0) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-08-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-023-03356-3
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Article ; Online: Electrocatalytic detection of ethanol and acetaldehyde by aminoxyl radicals: utilizing molecular catalysis for breath analysis.

Mayer, Mikayla N / Rafiee, Mohammad

The Analyst

2022 Volume 147, Issue 15, Page(s) 3420–3423

Abstract: Herein, the insights gleaned from mechanistic studies of aminoxyl catalyzed oxidation of alcohols and aldehydes were used for fabrication of a gas phase sensor for ethanol and acetaldehyde. This electrochemical sensor consists of an aminoxyl radical and ... ...

Abstract	Herein, the insights gleaned from mechanistic studies of aminoxyl catalyzed oxidation of alcohols and aldehydes were used for fabrication of a gas phase sensor for ethanol and acetaldehyde. This electrochemical sensor consists of an aminoxyl radical and graphene oxide so that its response and selectivity can be altered by tuning the basicity of the graphene oxide.
MeSH term(s)	Acetaldehyde ; Breath Tests ; Catalysis ; Ethanol/chemistry ; Oxidation-Reduction
Chemical Substances	Ethanol (3K9958V90M) ; Acetaldehyde (GO1N1ZPR3B)
Language	English
Publishing date	2022-07-22
Publishing country	England
Document type	Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/d2an00927g
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Article ; Online: Terahertz linear/non-linear anomalous Hall conductivity of moiré TMD hetero-nanoribbons as topological valleytronics materials.

Shayeganfar, Farzaneh / Ramazani, Ali / Habibiyan, Hamidreza / Rafiee Diznab, Mohammad

Scientific reports

2024 Volume 14, Issue 1, Page(s) 1581

Abstract: Twisted moiré van der Waals heterostructures hold promise to provide a robust quantum simulation platform for strongly correlated materials and realize elusive states of matter such as topological states in the laboratory. We demonstrated that the moiré ... ...

Abstract	Twisted moiré van der Waals heterostructures hold promise to provide a robust quantum simulation platform for strongly correlated materials and realize elusive states of matter such as topological states in the laboratory. We demonstrated that the moiré bands of twisted transition metal dichalcogenide (TMD) hetero-nanoribbons exhibit non-trivial topological order due to the tendency of valence and conduction band states in K valleys to form giant band gaps when spin-orbit coupling (SOC) is taken into account. Among the features of twisted WS[Formula: see text]/MoS[Formula: see text] and WSe[Formula: see text]/MoSe[Formula: see text], we found that the heavy fermions associated with the topological flat bands and the presence of strongly correlated states, enhance anomalous Hall conductivity (AHC) away from the magic angle. By band analysis, we showed that the topmost conduction bands from the ± K-valleys are perfectly flat and carry a spin/valley Chern number. Moreover, we showed that the non-linear anomalous Hall effect in moiré TMD hetero-nanoribbons can be used to manipulate terahertz (THz) radiation. Our findings establish twisted heterostructures of group-VI TMD nanoribbons as a tunable platform for engineering topological valley quantum phases and THz non-linear Hall conductivity.
Language	English
Publishing date	2024-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-51721-4
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Article ; Online: Periodic trends in the structural, electronic, and transport properties of electrenes.

Rafiee Diznab, Mohammad / Johnson, Erin R / Maassen, Jesse

Nanoscale

2023 Volume 15, Issue 28, Page(s) 12038–12047

Abstract: Two-dimensional layered electrides are a class of atomically thin materials in which the anion is an excess electron rather than a negatively charged ion. These excess electrons form delocalized sheets of charge surrounding each layer of the material. A ... ...

Abstract	Two-dimensional layered electrides are a class of atomically thin materials in which the anion is an excess electron rather than a negatively charged ion. These excess electrons form delocalized sheets of charge surrounding each layer of the material. A well-known example is Ca
Language	English
Publishing date	2023-07-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d3nr00304c
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Article ; Online: MicroRNA-125b as a valuable predictive marker for outcome after autologous hematopoietic stem cell transplantation.

Rafiee, Mohammad / Amiri, Fatemeh / Mohammadi, Mohammad Hossein / Hajifathali, Abbas

BMC cancer

2023 Volume 23, Issue 1, Page(s) 202

Abstract: Background: Relapse is a frequent occurrence in autologous hematopoietic stem cell transplantation (AHSCT), and early relapse after AHSCT results in poor survival and low quality of life. Predictive marker determination for AHSCT outcomes could be ... ...

Abstract	Background: Relapse is a frequent occurrence in autologous hematopoietic stem cell transplantation (AHSCT), and early relapse after AHSCT results in poor survival and low quality of life. Predictive marker determination for AHSCT outcomes could be helpful in the prevention of relapse through personalized medicine. Here the predictive value of circulatory microRNAs (miRs) expression for AHSCT outcomes was studied. Methods: 50 MM and lymphoma candidates for AHSCT participated in this study. Two plasma samples were obtained before AHSCT from each candidate; one before mobilization and the other after conditioning. Extracellular vesicles (EVs) were isolated by ultracentrifugation. miR-125b, miR-126, miR-150, and miR-155 expression were analyzed in both plasma and EVs using real time polymerase chain reaction analysis. Other data related to AHSCT and its outcomes were also collected. The predictive value of miRs and other factors for outcomes was assessed by multi-variant analysis. Results: By 90 weeks follow up after AHSCT, multi-variant and ROC analysis showed miR-125b as a predictive marker for relapse, high lactate dehydrogenase (LDH), and high erythrocyte sedimentation rate (ESR). The cumulative incidence of relapse, high LDH, and high ESR increased with an increase in circulatory miR-125b expression. Conclusion: miR-125b could be applicable in prognosis evaluation and also create a possible new targeted therapy opportunity for enhanced outcomes and survival after AHSCT. Trial registration: The study was retrospectively registered. Ethic code No: IR.UMSHA.REC.1400.541.
MeSH term(s)	Humans ; MicroRNAs ; Quality of Life ; Extracellular Vesicles ; Hematopoietic Stem Cell Transplantation ; L-Lactate Dehydrogenase
Chemical Substances	MicroRNAs ; L-Lactate Dehydrogenase (EC 1.1.1.27)
Language	English
Publishing date	2023-03-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2041352-X
ISSN	1471-2407 ; 1471-2407
ISSN (online)	1471-2407
ISSN	1471-2407
DOI	10.1186/s12885-023-10665-0
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Article: Responses of activated sludge under a short-term exposure to facial scrub microbeads: implications from treatment performance and higher-life microbial population dynamics.

Yazdanbakhsh, Ahmadreza / Rafiee, Mohammad / Mohammadi, Zahra

Water science and technology : a journal of the International Association on Water Pollution Research

2023 Volume 87, Issue 12, Page(s) 3031–3046

Abstract: In this study, four identical laboratory-scale sequencing batch reactors (SBRs) were continuously operated with different concentrations of microbeads (MBs) (5,000-15,000 MBs/L) to investigate the stress-responses of activated sludge under the MB ... ...

Abstract	In this study, four identical laboratory-scale sequencing batch reactors (SBRs) were continuously operated with different concentrations of microbeads (MBs) (5,000-15,000 MBs/L) to investigate the stress-responses of activated sludge under the MB exposure. It was found that the overall treatment performance (organic removal) of SBRs was fairly affected by short-term exposure to low levels of MBs; however, it was adversely affected as the concentration of MBs increased. The average concentration of mixed liquor suspended solids and heterotrophic bacteria in the reactor fed with 15,000 MBs/L were 16 and 30% less than in the pristine control reactor, respectively. Batch experiments further demonstrated that fairly low concentrations of MBs favored the development of dense microbial structures. Further increasing the MB concentrations to 15,000 MBs/L, however, distinctly weakened the settling performance of sludge. Morphological observations revealed suppressed uniformity, strength, and integrity of flocs reactors with the addition of MBs. Microbial community analyses revealed that the abundance of protozoan species declined 37.5, 58, and 64%, respectively, when SBRs were exposed to 5,000; 10,000; and 15,000 MBs/L as compared with the control reactor. The present work provided new insight into the possible effects of MBs on the performances and operational parameters of activated sludge.
MeSH term(s)	Sewage ; Microspheres ; Laboratories ; Microbiota ; Population Dynamics
Chemical Substances	Sewage
Language	English
Publishing date	2023-06-30
Publishing country	England
Document type	Journal Article
ZDB-ID	764273-8
ISSN	1996-9732 ; 0273-1223
ISSN (online)	1996-9732
ISSN	0273-1223
DOI	10.2166/wst.2023.183
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Article ; Online: Publisher Correction: Terahertz linear/non-linear anomalous Hall conductivity of moiré TMD hetero-nanoribbons as topological valleytronics materials.

Shayeganfar, Farzaneh / Ramazani, Ali / Habibiyan, Hamidreza / Diznab, Mohammad Rafiee

Scientific reports

2024 Volume 14, Issue 1, Page(s) 6179

Language	English
Publishing date	2024-03-14
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-56021-5
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Article ; Online: Role of particle local curvature in cellular wrapping.

Khosravanizadeh, Amir / Sens, Pierre / Mohammad-Rafiee, Farshid

Journal of the Royal Society, Interface

2022 Volume 19, Issue 196, Page(s) 20220462

Abstract: Cellular uptake through membranes plays an important role in adsorbing nutrients and fighting infection and can be used for nanomedicine developments. Endocytosis is one of the pathways of cellular uptake which associate with elastic deformation of the ... ...

Abstract	Cellular uptake through membranes plays an important role in adsorbing nutrients and fighting infection and can be used for nanomedicine developments. Endocytosis is one of the pathways of cellular uptake which associate with elastic deformation of the membrane wrapping around the foreign particle. The deformability of the membrane is strongly regulated by the presence of a cortical cytoskeleton placed underneath the membrane. It is shown that shape and orientation of the particles influence on their internalization. Here, we study the role of particle local curvature in cellular uptake by investigating the wrapping of an elastic membrane around a long cylindrical object with an elliptical cross-section. The membrane itself is adhered to a substrate mimicking the cytoskeleton. Membrane wrapping proceeds differently whether the initial contact occurs at the target's highly curved part (vertical) or along its long side (horizontal). We obtain a wrapping phase diagram as a function of the membrane-cytoskeleton and the membrane-target adhesion energy, which includes three distinct regimes (unwrapped, partially wrapped and fully wrapped), separated by two phase transitions. We also provide analytical expressions for the boundaries between the different regimes which confirm that the transitions strongly depend on the orientation and aspect ratio of the nanowire.
MeSH term(s)	Endocytosis ; Cytoskeleton/metabolism ; Biological Transport ; Nanowires ; Cell Membrane/metabolism
Language	English
Publishing date	2022-11-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2022.0462
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Article ; Online: Optimization of irrigation management and environmental assessment using the water cycle algorithm

Rafiee, Mohammad Rafie / Mahmoodi‐Eshkaftaki, Mahmood

Soil Use and Management. 2023 Apr., v. 39, no. 2 p.917-932

2023

Abstract: Obtaining high crop yields with limited water consumption requires optimal irrigation strategies based on comprehensive studies of the parameters of plant–environment interactions. Here, we used a structural equation modelling (SEM) to assess the ... ...

Abstract	Obtaining high crop yields with limited water consumption requires optimal irrigation strategies based on comprehensive studies of the parameters of plant–environment interactions. Here, we used a structural equation modelling (SEM) to assess the relationships among input irrigation factors and moderate factors to find an optimum water use efficiency (WUE) response factor, for outdoor and greenhouse cultivation of eggplant (Solanum melongena). The input irrigation factors (including irrigation interval, water salinity and environment) and the moderate factors (evapotranspiration, soil salinity, plant parameters, fruit parameters and crop yield) were used in water cycle algorithm (WCA) and genetic algorithm (GA) methods to optimize the water use efficiency. The optimization process included finding the best combination of irrigation factors and optimized eggplant cultivation. The structural equation modelling results indicate that irrigation interval negatively affected water use efficiency with a more dominant effect on plant parameters. Water salinity negatively affected the water use efficiency with a more dominant effect on soil salinity, crop yield and fruit parameters. Low salinity water was more effective than full irrigation to optimize the water use efficiency. The water cycle algorithm revealed that for outdoor cultivation, the optimal range of irrigation interval was 2–5 days and water salinity in the range of 0.8–2.2 ds/m. These factors optimized evapotranspiration (346.23–738.19 mm), soil salinity (4.16–9.45 ds/m), fruit parameters (33.81–35.12 cm) and crop yield (1715.7–2190.8 g/plant), as well as increasing the water use efficiency (3.08–4.89 g/(plant‐mm)). Both the water cycle algorithm and genetic algorithm yielded very close to optimal values. Two years of repeated experiments and the closeness of the optimal values using the algorithms confirmed that the optimal amounts are reliable.
Keywords	Solanum melongena ; administrative management ; algorithms ; crop yield ; eggplants ; environmental assessment ; equations ; evapotranspiration ; fruits ; greenhouse production ; hydrologic cycle ; irrigation rates ; irrigation scheduling ; soil salinity ; water salinity ; water use efficiency
Language	English
Dates of publication	2023-04
Size	p. 917-932.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	742151-5
ISSN	1475-2743 ; 0266-0032
ISSN (online)	1475-2743
ISSN	0266-0032
DOI	10.1111/sum.12875
Database	NAL-Catalogue (AGRICOLA)

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