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Article ; Online: Weighing single protein complexes on the go.

Vala, Milan / Piliarik, Marek

2021 Volume 18, Issue 10, Page(s) 1159–1160

Language	English
Publishing date	2021-10-04
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-021-01263-8
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Article ; Online: The modulatory effect of Lactobacillus gasseri ATCC 33323 on autophagy induced by extracellular vesicles of Helicobacter pylori in gastric epithelial cells in vitro.

Sadeghloo, Zahra / Saffarian, Parvaneh / Hakemi-Vala, Mojdeh / Sadeghi, Amir / Yadegar, Abbas

Microbial pathogenesis

2024 Volume 188, Page(s) 106559

Abstract: Helicobacter pylori has been recognized as a true pathogen, which is associated with various gastroduodenal diseases, and gastric adenocarcinoma. The crosstalk between H. pylori virulence factors and host autophagy remains challenging. H. pylori can ... ...

Abstract	Helicobacter pylori has been recognized as a true pathogen, which is associated with various gastroduodenal diseases, and gastric adenocarcinoma. The crosstalk between H. pylori virulence factors and host autophagy remains challenging. H. pylori can produce extracellular vesicles (EVs) that contribute to gastric inflammation and malignancy. Some probiotic strains have been documented to modulate cell autophagy process. This study was aimed to investigate the modulatory effect of cell-free supernatant (CFS) obtained from Lactobacillus gasseri ATCC 33323 on autophagy induced by H. pylori-derived EVs. EVs were isolated from two clinical H. pylori strains (BY-1 and OC824), and characterized using transmission electron microscopy (TEM) and dynamic light scattering (DLS). The viability of AGS cells was assessed after exposure to different concentrations of H. pylori EVs, and L. gasseri CFS. Based on MTT assay and Annexin V-FITC/PI staining, 50 μg/ml of H. pylori EVs and 10 % v/v of L. gasseri CFS were used for further cell treatment experiments. Autophagy was examined using acridin orange (AO) staining, RT-qPCR analysis for autophagy mediators (LC3B, ATG5, ATG12, ATG16L1, BECN1, MTOR, and NOD1), and western blotting for LC3B expression. H. pylori EVs were detected to range in size from 50 to 200 nm. EVs of both H. pylori strains and L. gasseri CFS showed no significant effect on cell viability as compared to untreated cells. H. pylori EVs promoted the development of acidic vesicular organelles and the expression of autophagy-related genes (LC3B, ATG5, ATG12, ATG16L1, BECN1, and NOD1), and decreased the expression of MTOR in AGS cells at 12 and 24 h time periods. In addition, the production of LC3B was increased following 12 h of treatment in AGS cells. In contrast, L. gasseri CFS effectively inhibited EVs-induced autophagy, as evidenced by reduced acidic vesicular organelle formation and modulation of autophagy markers. Our study indicated that L. gasseri CFS can effectively suppress H. pylori EV-induced autophagy in AGS cells. Further investigations are required to decipher the mechanism of action L. gasseri CFS and its metabolites on autophagy inhibition induced by H. pylori.
MeSH term(s)	Humans ; Helicobacter pylori/genetics ; Lactobacillus gasseri ; Epithelial Cells ; Autophagy ; Extracellular Vesicles ; TOR Serine-Threonine Kinases ; Helicobacter Infections/therapy
Chemical Substances	TOR Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2024-01-23
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2024.106559
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Article ; Online: Complete Set of Diketopyrrolopyrrole Centrosymmetrical Cofacial Stacked Pairs.

Luňák, Stanislav / Weiter, Martin / Vala, Martin

Chemphyschem : a European journal of chemical physics and physical chemistry

2022 Volume 23, Issue 21, Page(s) e202200252

Abstract: Stacked centrosymmetrical dimers and simultaneously H-bonded and stacked hexamers of thiophene-substituted diketopyrrolopyrrole (ThDPP) were studied using DFT as models for crystals with slipped-stacked molecules in 1D columns. Eight stacked dimer ... ...

Abstract	Stacked centrosymmetrical dimers and simultaneously H-bonded and stacked hexamers of thiophene-substituted diketopyrrolopyrrole (ThDPP) were studied using DFT as models for crystals with slipped-stacked molecules in 1D columns. Eight stacked dimer arrangements were found, six of which are driven by the minimisation of electron repulsion and realised by placing the partially negatively charged atoms of the diketopyrrolopyrrole rings below the centre of an adjacent thiophene ring. Four of these stacks are related to N,N'-dialkylated derivatives of ThDPP found in the literature, while a further one is related to an N,N'-diacylated derivative. An analogous set of eight stacks was discovered computationally for phenyl-substituted DPP (PhDPP), four of which are known among H-bonded DPP pigments, and one more among N,N'-dialkylated PhDPP derivatives. The results shed more light on the mechanisms that drive the formation of stacks between nonaromatic (DPP) and aromatic (Th, Ph) rings. The excitation energies of the lowest four singlet states computed by TD DFT enabled excitonic coupling and energy separation between Frenkel-resonance-type and charge-transfer states to be established, depending on the equilibrium stack geometry.
MeSH term(s)	Electrons ; Thiophenes
Chemical Substances	diketopyrrolopyrrole dye ; Thiophenes
Language	English
Publishing date	2022-07-28
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2025223-7
ISSN	1439-7641 ; 1439-4235
ISSN (online)	1439-7641
ISSN	1439-4235
DOI	10.1002/cphc.202200252
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Article ; Online: Multiple beam interference lithography: A tool for rapid fabrication of plasmonic arrays of arbitrary shaped nanomotifs.

Vala, M / Homola, J

Optics express

2016 Volume 24, Issue 14, Page(s) 15656–15665

Abstract: A novel method enabling rapid fabrication of 2D periodic arrays of plasmonic nanoparticles across large areas is presented. This method is based on the interference of multiple coherent beams originating from diffraction of large-diameter collimated beam ...

Abstract	A novel method enabling rapid fabrication of 2D periodic arrays of plasmonic nanoparticles across large areas is presented. This method is based on the interference of multiple coherent beams originating from diffraction of large-diameter collimated beam on a transmission phase mask. Mutual orientation of the interfering beams is determined by parameters of the used phase mask. Herein, parameters of the phase mask (periods and modulation depth) are selected to yield an interference pattern with high contrast and narrow well-separated maxima. Finally, multiple beam interference lithography (MBIL)-based fabrication of periodic plasmonic arrays with selected nanomotifs including discs, disc dimers, rods and bowtie antennas is demonstrated.
Language	English
Publishing date	2016-07-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.24.015656
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Article ; Online: Evaluation of the antibacterial effect of hydroalcoholic extract of the galls of

Tabibzadeh Noori, Zohreh / Tabatabaei Rad, Mohadese / Hakemi Vala, Mojdeh / Karimi, Mehrdad / Esmaeil Nejad, Azadeh

Journal of advanced periodontology & implant dentistry

2023 Volume 15, Issue 1, Page(s) 35–41

Abstract: Background: Aggregatibacter actinomycetemcomitans: Methods: The hydroalcoholic extract of Qi was obtained by the maceration method, and Aa bacterial strain was cultured. The inhibition zone diameter was measured through the agar well diffusion method. ...

Abstract	Background: Aggregatibacter actinomycetemcomitans Methods: The hydroalcoholic extract of Qi was obtained by the maceration method, and Aa bacterial strain was cultured. The inhibition zone diameter was measured through the agar well diffusion method. Also, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values were determined by the broth microdilution method. All the experiments were repeated three times. 0.2% CHX was used as a control. Results: The inhibition zone diameter of Aa increased with increasing concentration of Qi extract. While MIC and MBC values for CHX were 0.0039 and 0.0078 mg/mL, respectively, both MIC and MBC values of the Qi extract for this bacterium were similar, i.e., 2.5 mg/mL, which was significantly higherd. Conclusion: Since other in vivo studies have confirmed the other properties of this extract and its safety in terms of cytotoxicity and mutagenicity, hydroalcoholic extract of Qi may be used in mouthwashes or local delivery systems to affect periodontal biofilm.
Language	English
Publishing date	2023-04-05
Publishing country	Iran
Document type	Journal Article
ISSN	2645-5390
ISSN (online)	2645-5390
DOI	10.34172/japid.2023.006
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Article ; Online: Evaluation of Vascular Endothelial Growth Factor Gene Expression in Recellularized Liver Tissue by Mouse Embryo Fibroblast.

Homayoon Vala, Motahare / Bagheri, Hamed / Zinat, Sargazi / Bakhtiary, Negar / Pourbeiranvand, Shahram / Salehnia, Mojdeh

Iranian biomedical journal

2023 Volume 27, Issue 6, Page(s) 340–348

Abstract: Background: The aim of the present study was to evaluate alterations in the vegf gene expression as an angiogenic factor in mouse embryo fibroblasts seeded on the decellularized liver fragments.: Methods: Liver tissue samples (n = 10) collected from ... ...

Abstract	Background: The aim of the present study was to evaluate alterations in the vegf gene expression as an angiogenic factor in mouse embryo fibroblasts seeded on the decellularized liver fragments. Methods: Liver tissue samples (n = 10) collected from adult male mice were randomly divided into decellularized and native control groups. Tissues were decellularized by treating with 1% Triton X-100 and 0.1% SDS for 24 hours and assessed by H&E staining and SEM. Then DNA content analysis and toxicity tests were performed. By centrifugation, DiI-labeled mouse embryo fibroblasts were seeded on each scaffold and cultured for one week. The recellularized scaffolds were studied by H&E staining, SEM, and LSCM. After RNA extraction and cDNA synthesis, the expression of the vegf gene in these samples was investigated using real-time RT-PCR. Results: Our observations showed that the decellularized tissues had morphology and porous structure similar to the control group, and their DNA content significantly reduced (p < 0.05) and reached to 4.12% of the control group. The MTT test indicated no significant cellular toxicity for the decellularized scaffolds. Light microscopy, SEM, and LSCM observations confirmed the attachment and penetration of embryonic fibroblast cells on the surface and into different depths of the scaffolds. There was no statistically significant difference in terms of vegf gene expression in the cultured cells in the presence and absence of a scaffold. Conclusion: The reconstructed scaffold had no effect on vegf gene expression. Decellularized mouse liver tissue recellularized by embryonic fibroblasts could have an application in regenerative medicine.
MeSH term(s)	Male ; Mice ; Animals ; Tissue Scaffolds/chemistry ; Vascular Endothelial Growth Factor A/genetics ; Liver ; DNA ; Gene Expression ; Tissue Engineering ; Extracellular Matrix
Chemical Substances	Vascular Endothelial Growth Factor A ; DNA (9007-49-2)
Language	English
Publishing date	2023-11-01
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2489282-8
ISSN	2008-823X ; 1028-852X
ISSN (online)	2008-823X
ISSN	1028-852X
DOI	10.61186/ibj.3862
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Article ; Online: In silico

Amiri, Parisa / Hakemi-Vala, Mojdeh / Nazarian, Ahmad / Barneh, Farnoosh / Pooshang Bagheri, Kamran

Current pharmaceutical design

2023 Volume 29, Issue 26, Page(s) 2101–2109

Abstract: Introduction: Extensively and multi-drug resistant isolates of bacteria (MDR, XDR) have caused significant health problems and are responsible for high morbidity and mortality as well. In this critical condition, the discovery, design, or development of ...

Abstract	Introduction: Extensively and multi-drug resistant isolates of bacteria (MDR, XDR) have caused significant health problems and are responsible for high morbidity and mortality as well. In this critical condition, the discovery, design, or development of new antibiotics is of great concern. According to this necessity, antimicrobial peptides (AMPs) suggested as promising agents. Accordingly, this study aims to evaluate the GKY25 peptide to develop its future antibacterial applications as well as confirmation of LPS neutralization. Methods: Predictions of 3D structure and helical wheel projection analysis of the peptide were performed by ITASSER and Heliquest servers. Binding affinity and antibacterial activity were performed using molecular docking and CAMP Results: GKY25 was predicted as an alpha-helical peptide, and its helicity showed probable projection of hydrophobic and positively-charged amino acid residues. Docking studies showed binding affinity of GKY25 peptide to gram-positive and outer and inner gram-negative bacterial membranes as -5.7, -6.8, and -4 kcal/mole, respectively. CAMP Conclusion: Gathering all
Language	English
Publishing date	2023-10-03
Publishing country	United Arab Emirates
Document type	Journal Article
ZDB-ID	1304236-1
ISSN	1873-4286 ; 1381-6128
ISSN (online)	1873-4286
ISSN	1381-6128
DOI	10.2174/1381612829666230905143544
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Article ; Online: Flexible method based on four-beam interference lithography for fabrication of large areas of perfectly periodic plasmonic arrays.

Vala, M / Homola, J

Optics express

2014 Volume 22, Issue 15, Page(s) 18778–18789

Abstract: A novel nanofabrication technique based on 4-beam interference lithography is presented that enables the preparation of large macroscopic areas (>50 mm2) of perfectly periodic and defect-free two-dimensional plasmonic arrays of nanoparticles as small as ... ...

Abstract	A novel nanofabrication technique based on 4-beam interference lithography is presented that enables the preparation of large macroscopic areas (>50 mm2) of perfectly periodic and defect-free two-dimensional plasmonic arrays of nanoparticles as small as 100 nm. The technique is based on a special interferometer, composed of two mirrors and a sample with photoresist that together form a right-angled corner reflector. In such an interferometer, the incoming expanded laser beam is split into four interfering beams that yield an interference pattern with rectangular symmetry. The interferometer allows setting the periods of the array from about 220 nm to 1500 nm in both directions independently through the rotation of the corner-reflector assembly around horizontal and vertical axes perpendicular to the direction of the incident beam. Using a theoretical model, the implementation of the four-beam interference lithography is discussed in terms of the optimum contrast as well as attainable periods of the array. Several examples of plasmonic arrays (on either glass or polymer substrate layers) fabricated by this technique are presented.
Language	English
Publishing date	2014-07-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.22.018778
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Article: Rifampin resistance among individuals with extrapulmonary tuberculosis: 4 years of experience from a reference laboratory.

Baghbanbashi, S / Mousavi, S Mohammad J / Dabiri, H / Hakemi-Vala, M / Goudarzi, H / Hamzehloo, G / Amini, S / Nasiri, M J

New microbes and new infections

2021 Volume 40, Page(s) 100841

Abstract: Information is limited about the drug resistance patterns in extrapulmonary tuberculosis (EPTB) in Iran. This study aimed to determine the prevalence of EPTB and to investigate the drug-resistance pattern ... ...

Abstract	Information is limited about the drug resistance patterns in extrapulmonary tuberculosis (EPTB) in Iran. This study aimed to determine the prevalence of EPTB and to investigate the drug-resistance pattern in
Language	English
Publishing date	2021-01-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2750179-6
ISSN	2052-2975
ISSN	2052-2975
DOI	10.1016/j.nmni.2021.100841
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Article ; Online: Fast killing kinetics, significant therapeutic index, and high stability of melittin-derived antimicrobial peptide.

Akbari, Reza / Hakemi Vala, Mojdeh / Sabatier, Jean-Marc / Pooshang Bagheri, Kamran

Amino acids

2022 Volume 54, Issue 9, Page(s) 1275–1285

Abstract: The emergence of multidrug-resistant (MDR) bacteria is a major challenge for antimicrobial chemotherapy. Concerning this issue, antimicrobial peptides (AMPs) have been presented as novel promising antibiotics. Our previous de novo designed melittin- ... ...

Abstract	The emergence of multidrug-resistant (MDR) bacteria is a major challenge for antimicrobial chemotherapy. Concerning this issue, antimicrobial peptides (AMPs) have been presented as novel promising antibiotics. Our previous de novo designed melittin-derived peptides (MDP1 and MDP2) indicated their potential as peptide drug leads. Accordingly, this study was aimed to evaluate the kinetics of activity, toxicity, and stability of MDP1 and MDP2 as well as determination of their structures. The killing kinetics of MDP1 and MDP2 demonstrate that all bacterial strains were rapidly killed. MDP1 and MDP2 were ca. 100- and 26.6-fold less hemolytic than melittin and found to be respectively 72.9- and 41.6-fold less cytotoxic than melittin on the HEK293 cell line. MDP1 and MDP2 showed 252- and 132-fold improvement in their therapeutic index in comparison to melittin. MDP1 and MDP2 sustained their activities in the presence of human plasma and were found to be ca. four to eightfold more stable than melittin. Spectropolarimetry analysis of MDP1 and MDP2 indicates that the peptides adopt an alpha-helical structure predominantly. According to the fast killing kinetics, significant therapeutic index, and high stability of MDP1, it could be considered as a drug lead in a mouse model of septicemia infections.
MeSH term(s)	Animals ; Anti-Bacterial Agents/chemistry ; Antimicrobial Peptides ; HEK293 Cells ; Humans ; Kinetics ; Melitten/chemistry ; Melitten/pharmacology ; Mice ; Microbial Sensitivity Tests ; Peptides/chemistry ; Therapeutic Index
Chemical Substances	Anti-Bacterial Agents ; Antimicrobial Peptides ; Peptides ; Melitten (20449-79-0)
Language	English
Publishing date	2022-07-02
Publishing country	Austria
Document type	Journal Article
ZDB-ID	1121341-3
ISSN	1438-2199 ; 0939-4451
ISSN (online)	1438-2199
ISSN	0939-4451
DOI	10.1007/s00726-022-03180-2
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