scholarly journals In silico identification and expression analysis of Metal-nicotianamine transporter (YSL3) and Oligopeptide transporter 3 (OPT3) under Cd stress in Brassica oleracea var. acephala

2020 ◽  
Vol 98 (4) ◽  
pp. 516-523
Author(s):  
Jasmin Sutkovic ◽  
Ajdina Karic ◽  
Ahmet Yildirim
Keyword(s):  
Brassica Oleracea ◽  
Expression Analysis ◽  
In Silico ◽  
Cadmium Stress ◽  
Cd Stress ◽  
Long Distance ◽  
Oligopeptide Transporter ◽  
Metal Transporter ◽  
Nitrogen Mobilization

Background: Metal-nicotianamine transporter (YSL) family protein belongs to the oligopeptide heavy metal transporter group, as characterized in Arabidopsis thaliana. Oligopeptide transporters (OPTs) are a group of membrane-localized proteins, involved in different transport mechanisms, contributing to nitrogen mobilization, glutathione transport and long-distance metal distribution. Metal-nicotianamine transporter gene 3 (YSL3) incorporates the oligopeptide transporter domain, found to transfer several heavy metals in diverse plant species, and among them cadmium transport in Brassica oleracea. Objective: To evaluate and confirm the expression of Metal-nicotianamine transporter (YSL3) under cadmium stress. Studied species: Brassica oleracea var. acephala Study site and dates: Brassica oleracea var. acephala samples were collected from Blagaj region, Bosnia and Herzegovina. Methods: Through a simple bioinformatic approach the interactome partner of Metal-nicotianamine transporter (YSL3) was discovered and annotated. Oligopeptide transporter 3 (OPT3) and Metal-nicotianamine transporter (YSL3) genes were checked for expression levels under cadmium stress. Results: We have identified a strong interacting partner of YSL3, later confirmed as Oligopeptide transporter 3 (OPT3) protein in Brassica oleracea. The in vitro expression analysis by using a qRT-PCR revealed a significant upregulation of YSL3 and OPT3, during Cd stress. Conclusions: These findings indicate that the represented in-silico approach, followed by in vitro gene expression study, successfully confirmed YSL3 and identified OPT3 as a new gene, in correlation to cadmium stress.

scholarly journals IN SILICO DESIGN, SYNTHESIS AND EVALUATION OF IN VITRO GLUCOSE UPTAKE, GENE EXPRESSION, AND α-GLUCOSIDASE INHIBITORY ACTIVITY OF NOVEL 2-AMINOBENZIMIDAZOLE DERIVATIVES

2019 ◽  
pp. 107-114
Author(s):  
SREEJA S ◽  
ANTON SMITH A ◽  
MATHAN S
Keyword(s):  
Gene Expression ◽  
Glucose Uptake ◽  
Expression Analysis ◽  
Inhibitory Activity ◽  
In Silico ◽  
Gene Expression Analysis ◽  
Lethal Dose ◽  
Standard Drug ◽  
Lipinski’S Rule

Objective: The present study was aimed to design and evaluate the antidiabetic potential of novel 2-aminobenzimidazole derivatives by in silico method. Materials and Methods: Various in silico tools such as Chemsketch, Molinspiration, Prediction of activity spectra for substances, OpenBabel, Discovery Studio was used in the designing and evaluation of the biological activity. The retrieved hits were further filtered by absorption, distribution, metabolism, and excretion descriptors. The designed molecules having required physicochemical properties, drug-likeness, and obeying Lipinski’s rule of five were selected for the synthesis. The synthesized compounds were subjected to determination of yield, melting point and characterized by infrared, 1HNMR, 13CNMR, and mass spectroscopic methods. The selected derivatives were subjected to in vitro glucose uptake, 50% lethal dose (LD50) determination, gene expression analysis, and α-glucosidase inhibitory assay. Results: Totally, 32 novel analogs of 2-aminobenzimidazole were designed and 17 compounds were selected for docking analysis; and finally, five derivatives (3a, 3c, 3e, 3f, and 3h) were selected for synthesis. Among them, the compounds 3a and 3f were selected for in vitro glucose uptake analysis. Finally, the compound 3f was selected for LD50 determination, gene expression analysis, and α-glucosidase inhibitory assay. The selected derivative 3f showed a significant α-glucosidase inhibitory activity compared with the standard drug acarbose. Conclusion: These results are useful for further investigation in the future, and hopefully, these studies could discover a new specific leads in antidiabetic category as α-glucosidase inhibitor.

scholarly journals Antioxidants enzyme activity in Brassica oleracea var. acephala under cadmium stress

2020 ◽  
Vol 1 (1) ◽  
pp. 1-13
Author(s):  
Kanita Šabanović ◽  
Ahmet Yildirim ◽  
Jasmin Šutković
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Brassica Oleracea ◽  
Cadmium Stress ◽  
Heavy Metal Stress ◽  
Heavy Metal Accumulation ◽  
Significant Activity ◽  
Antioxidants Enzymes ◽  
Hybrid Variety

When a plant is under heavy metals stress, it has different mechanism of coping with it. Brassica oleracea var. acephala (kale) is a plant that has an ability of heavy metal accumulation and removal of heavy metals from the ground. The plants were  exposed to 50, 100, 200, and 500 μM of CdCl2 for 5days, in controlled in vitro conditions. Root length was measured to confirm the Cd effect on plant growth. There are five key antioxidants enzymes responsible for the regulation of heavy metals stress: superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), Peroxidase (POD) and Polyphenol oxidase (PPO). All enzymes showed significant activity, especially triggered by 500 μM CdCl2 in both varieties. The domestic sorts seem more resistant if compared to hybrid variety, showing significant lower expression of antioxidants enzymes at higher concentrations.  In general, significant percentage of enzymes is more expressed in the hybrid Italian sort, Nero di Toscana, indicating the ability of domestic sorts to be more resistant to heavy metal stress.

scholarly journals PDF1.5 Enhances Adaptation to Low Nitrogen Levels and Cadmium Stress

2021 ◽  
Vol 22 (19) ◽  
pp. 10455
Author(s):  
Zhimin Wu ◽  
Dong Liu ◽  
Ningyan Yue ◽  
Haixing Song ◽  
Jinsong Luo ◽  
...  
Keyword(s):  
Cadmium Stress ◽  
Nitrate Transporter ◽  
Cd Stress ◽  
Metallic Elements ◽  
Histochemical Analysis ◽  
Cd Accumulation ◽  
Nitrogen Levels ◽  
Metal Transporter ◽  
Localization Analysis ◽  
Low Nitrogen

Environmental acclimation ability plays a key role in plant growth, although the mechanism remains unclear. Here, we determined the involvement of Arabidopsis thaliana PLANT DEFENSIN 1 gene AtPDF1.5 in the adaptation to low nitrogen (LN) levels and cadmium (Cd) stress. Histochemical analysis revealed that AtPDF1.5 was mainly expressed in the nodes and carpopodium and was significantly induced in plants exposed to LN conditions and Cd stress. Subcellular localization analysis revealed that AtPDF1.5 was cell wall- and cytoplasm-localized. AtPDF1.5 overexpression significantly enhanced adaptation to LN and Cd stress and enhanced the distribution of metallic elements. The functional disruption of AtPDF1.5 reduced adaptations to LN and Cd stress and impaired metal distribution. Under LN conditions, the nitrate transporter AtNRT1.5 expression was upregulated. Nitrate transporter AtNRT1.8 expression was downregulated when AtPDF1.5 was overexpressed, resulting in enhanced transport of NO3− to shoots. In response to Cd treatment, AtPDF1.5 regulated the expression of metal transporter genes AtHMP07, AtNRAMP4, AtNRAMP1, and AtHIPP3, resulting in higher Cd accumulation in the shoots. We conclude that AtPDF1.5 is involved in the processing or transmission of signal substances and plays an important role in the remediation of Cd pollution and LN adaptation.

IN VITRO/IN SILICO CHARACTERIZATION OF ACTIVE AND PASSIVE STRESSES IN CARDIAC MUSCLE

2012 ◽  
Vol 10 (2) ◽  
pp. 171-188 ◽  
Author(s):  
Markus Boel ◽  
Oscar J. Abilez ◽  
Ahmed N Assar ◽  
Christopher K. Zarins ◽  
Ellen Kuhl
Keyword(s):  
Cardiac Muscle ◽  
In Silico ◽  
In Silico Characterization

Role of 4-O Galloylchlorogenic Acid in Lung Cancer- An Insilico Approach

2017 ◽  
Vol 9 (5) ◽  
Author(s):  
Jaynthy C. ◽  
N. Premjanu ◽  
Abhinav Srivastava
Keyword(s):  
Lung Cancer ◽  
Cell Proliferation ◽  
In Silico ◽  
Computational Study ◽  
Regulation Mechanism ◽  
Down Regulation ◽  
Fruit Extract ◽  
In Vitro Techniques ◽  
Discovery Studio

Cancer is a major disease with millions of patients diagnosed each year with high mortality around the world. Various studies are still going on to study the further mechanisms and pathways of the cancer cell proliferation. Fucosylation is one of the most important oligosaccharide modifications involved in cancer and inflammation. In cancer development increased core fucosylation by FUT8 play an important role in cell proliferation. Down regulation of FUT8 expression may help cure lung cancer. Therefore the computational study based on the down regulation mechanism of FUT8 was mechanised. Sapota fruit extract, containing 4-Ogalloylchlorogenic acid was used as the inhibitor against FUT-8 as target and docking was performed using in-silico tool, Accelrys Discovery Studio. There were several conformations of the docked result, and conformation 1 showed 80% dock score between the ligand and the target. Further the amino acids of the inhibitor involved in docking were studied using another tool, Ligplot. Thus, in-silico analysis based on drug designing parameters shows that the fruit extract can be studied further using in-vitro techniques to know its pharmacokinetics.

Discovery of New AKT1 Inhibitors by Combination of In silico Structure Based Virtual Screening Approaches and Biological Evaluations

2019 ◽  
Author(s):  
Filip Fratev ◽  
Denisse A. Gutierrez ◽  
Renato J. Aguilera ◽  
suman sirimulla
Keyword(s):  
Virtual Screening ◽  
Success Rate ◽  
Protein Interactions ◽  
In Silico ◽  
Biological Data ◽  
In Vitro Binding ◽  
Vitro Binding ◽  
Screening Protocol ◽  
Screening Approaches

AKT1 is emerging as a useful target for treating cancer. Herein, we discovered a new set of ligands that inhibit the AKT1, as shown by in vitro binding and cell line studies, using a newly designed virtual screening protocol that combines structure-based pharmacophore and docking screens. Taking together with the biological data, the combination of structure based pharamcophore and docking methods demonstrated reasonable success rate in identifying new inhibitors (60-70%) proving the success of aforementioned approach. A detail analysis of the ligand-protein interactions was performed explaining observed activities.<br>

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