scholarly journals Beneficial Microorganisms to Control the Gray Mold of Grapevine: From Screening to Mechanisms

2021 ◽  
Vol 9 (7) ◽  
pp. 1386
Author(s):  
Zakaria Amarouchi ◽  
Qassim Esmaeel ◽  
Lisa Sanchez ◽  
Cédric Jacquard ◽  
Majida Hafidi ◽  
...  
Keyword(s):  
In Silico Analysis ◽  
Antimicrobial Effect ◽  
Gray Mold ◽  
Vitis Vinifera L ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
In Vivo Test ◽  
Chemical Products ◽  
Silico Analysis

In many vineyards around the world, Botrytis cinerea (B. cinerea) causes one of the most serious diseases of aerial grapevine (Vitis vinifera L.) organs. The control of the disease relies mainly on the use of chemical products whose use is increasingly challenged. To develop new sustainable methods to better resist B. cinerea, beneficial bacteria were isolated from vineyard soil. Once screened based on their antimicrobial effect through an in vivo test, two bacterial strains, S3 and S6, were able to restrict the development of the pathogen and significantly reduced the Botrytis-related necrosis. The photosynthesis analysis showed that the antagonistic strains also prevent grapevines from considerable irreversible PSII photo-inhibition four days after infection with B. cinerea. The 16S rRNA gene sequences of S3 exhibited 100% similarity to Bacillus velezensis, whereas S6 had 98.5% similarity to Enterobacter cloacae. On the other hand, the in silico analysis of the whole genome of isolated strains has revealed the presence of “biocontrol-related” genes supporting their plant growth and biocontrol activities. The study concludes that those bacteria could be potentially useful as a suitable biocontrol agent in harvested grapevine.

Investigation of indole functionalized pyrazoles and oxadiazoles as anti-inflammatory agents: synthesis, in-vivo, in-vitro and in-silico analysis

2021 ◽  
pp. 105068
Author(s):  
Devendra Kumar ◽  
Ravi Ranjan Kumar ◽  
Shelly Pathania ◽  
Pankaj Kumar Singh ◽  
Sourav Kalra ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Anti Inflammatory ◽  
Silico Analysis

In-Silico Analysis to Identify Potential Inhibitors Against the Protein NSP12 of SARS-CoV-2

2021 ◽  
Vol 6 (3) ◽  
pp. 48-60
Author(s):  
Hima Vyshnavi ◽  
Gayathri S. S. ◽  
Shahanas Naisam ◽  
Suvanish Kumar ◽  
Nidhin Sreekumar
Keyword(s):  
In Silico ◽  
Interaction Analysis ◽  
In Silico Analysis ◽  
Drug Efficacy ◽  
Drug Candidate ◽  
In Vivo Analysis ◽  
The Stability ◽  
Potential Inhibitors ◽  
Silico Analysis

In this pandemic condition, a drug candidate which is effective against COVID-19 is very much desired. This study initiates an in silico analysis to screen small molecules such as phytochemicals, drug metabolites, and natural metabolites against Nsp12 (a catalytic unit for RNA transcription and replication). Molecular interaction analysis of 6M71 was carried out against 2,860 ligands using Schrodinger Glide software. After docking analysis, the top 10 molecules (Glide score) were subjected to MD simulation for validating the stability. It resulted in top 10 compounds with high binding affinities with the target molecule NSP 12. Out of these, top 3 compounds including PSID_08_LIG3 (HMDB0133544), PSID_08_LIG4 (HMDB0132898), and PSID_08_LIG9 (HMDB0128199) show better Glide scores, better H-bond interaction, better MMGBSA value and stability on dynamic simulation after analysis of the results. The suggested ligands can be postulated as effective antiviral drugs against COVID-19. Further in vivo analysis is needed for validating the drug efficacy.

In-Silico Analysis to Identify Potent Quinoline Analogues Against Multi-Targets of SARS-CoV-2

2021 ◽  
Vol 6 (4) ◽  
pp. 25-37
Author(s):  
Shahanas Naisam ◽  
Viji V.S. ◽  
Suvanish Kumar ◽  
Nidhin Sreekumar
Keyword(s):  
Interaction Analysis ◽  
In Silico Analysis ◽  
Preventive Treatment ◽  
Drug Molecule ◽  
Current Outbreak ◽  
In Vivo Analysis ◽  
Effective Drugs ◽  
Silico Analysis

In the current outbreak of COVID-19, various studies have been conducted all over the world to develop effective drugs against the virus. Recent studies have shown that hydroxychloroquine, chloroquine (antimalarial drugs), isoflavones, flavonoids, etc. have potent antiviral properties, and few have been proven as effective drugs for the preventive treatment of COVID-19. But their exact action against SARS-CoV-2 is still unknown. The strategy of this study is the virtual screening of quinoline analogues, design new ligand molecules, perform molecular interaction analysis, their MD validation against multi targets (Spike-ACE2, TMPRSS2, and Spike Protein) of SARS-CoV-2, and to suggest the most promising and effective drug molecule. Hydroxychloroquine and chloroquine were considered as the reference molecules in this study. A ligand N-[4-(3-Benzylideneazetidine-1-carbonyl)phenyl]quinoline-8-sulfonamide interacting with TMPRSS2 shows better interaction among the list even after MD validation. Further in-vitro and in-vivo analysis of this study is needed for future validation.

An in vivo and in silico analysis of novel variation in TMBIM6 gene affecting cardiopulmonary traits of Indian goats

2020 ◽  
Vol 88 ◽  
pp. 102491
Author(s):  
Lipi Lekha Swain ◽  
Chinmoy Mishra ◽  
Siddhant Sekhar Sahoo ◽  
Gangadhar Nayak ◽  
Sukanta Kumar Pradhan ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis ◽  
Novel Variation

scholarly journals Predicting In Vivo Responses to Biomaterials via Combined In Vitro and In Silico Analysis

2015 ◽  
Vol 21 (2) ◽  
pp. 148-159 ◽  
Author(s):  
Matthew T. Wolf ◽  
Yoram Vodovotz ◽  
Stephen Tottey ◽  
Bryan N. Brown ◽  
Stephen F. Badylak
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis

scholarly journals Empirical Testing of 16S rRNA Gene PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy Not Suggested by In Silico Analysis

2009 ◽  
Vol 75 (9) ◽  
pp. 2677-2683 ◽  
Author(s):  
Sergio E. Morales ◽  
William E. Holben
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Quantitative Pcr ◽  
In Silico ◽  
In Silico Analysis ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Empirical Testing ◽  
Specific Target ◽  
Silico Analysis

ABSTRACT Phylogenetic and “fingerprinting” analyses of the 16S rRNA genes of prokaryotes have been a mainstay of microbial ecology during the last two decades. However, many methods and results from studies that rely on the 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received only cursory or even no validation. To directly examine the efficacy and specificity of 16S rRNA gene-based primers for phylum-, class-, and operational taxonomic unit-specific target amplification in quantitative PCR, we created a collection of primers based solely on an extensive soil bacterial 16S rRNA gene clone library containing ∼5,000 sequences from a single soil sample (i.e., a closed site-specific library was used to create PCR primers for use at this site). These primers were initially tested in silico prior to empirical testing by PCR amplification of known target sequences and of controls based on disparate phylogenetic groups. Although all primers were highly specific according to the in silico analysis, the empirical analyses clearly exhibited a high degree of nonspecificity for many of the phyla or classes, while other primers proved to be highly specific. These findings suggest that significant care must be taken when interpreting studies whose results were obtained with target specific primers that were not adequately validated, especially where population densities or dynamics have been inferred from the data. Further, we suggest that the reliability of quantification of specific target abundance using 16S rRNA-based quantitative PCR is case specific and must be determined through rigorous empirical testing rather than solely in silico.

scholarly journals In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae

2013 ◽  
Vol 7 (1) ◽  
pp. 24 ◽  
Author(s):  
Flavio Amara ◽  
Riccardo Colombo ◽  
Paolo Cazzaniga ◽  
Dario Pescini ◽  
Attila Csikász-Nagy ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Repair Pathway ◽  
Post Replication Repair ◽  
Silico Analysis

scholarly journals A model of stem cell population dynamics: in silico analysis and in vivo validation

2012 ◽  
Vol 125 (1) ◽  
pp. e1-e1 ◽  
Author(s):  
Y. Setty ◽  
D. Dalfo ◽  
D. Z. Korta ◽  
E. J. A. Hubbard ◽  
H. Kugler
Keyword(s):  
Population Dynamics ◽  
Stem Cell ◽  
Cell Population ◽  
In Silico ◽  
In Silico Analysis ◽  
Stem Cell Population ◽  
Cell Population Dynamics ◽  
Silico Analysis ◽  
In Vivo Validation

scholarly journals Antimicrobial Effect of Zataria Essential Oil on the Skin Bacteria in Wistar Rats

2020 ◽  
Vol 10 (1) ◽  
pp. 56-67
Author(s):  
Soheila Faramarz Isfahanian ◽  
◽  
Maryam Sadrnia ◽  
Sima Nasri ◽  
Hamid Sobhanian ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Essential Oil ◽  
Staphylococcus Epidermidis ◽  
Wistar Rats ◽  
Antimicrobial Effect ◽  
Bacterial Strains ◽  
Antimicrobial Effects ◽  
Skin Bacteria ◽  
Allergy Test

Objective: Zataria is one of the native plants of Iran which is widely used for the treatment of diseases among Iranians. In this study, we investigated the antimicrobial effects of Zataria essential oil on the skin bacteria in rats. Methods: Bacterial strains were isolated from the skin of 6 wistar rats and the antimicrobial effects of Zataria essential oil were evaluated by disk diffusion and microbroth dilution methods. In-vivo tests were performed to evaluate the antimicrobial effect of the essential oil by microbial culture as well as allergy tests on the skin of experimental rats compared to controls. Results: Three bacterial strains were isolated from the skin of rats identified as Staphylococcus aureus, Corynebacterium and Staphylococcus epidermidis. Minimum Growth Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) for the two strains of Staphylococcus aureus and Corynebacterium were obtained 0.39 and 0.78 mg/ml, while for Staphylococcus epidermidis, they were 0.195 and 0.39 mg/ml, respectively. In-vivo test results showed the antibacterial effect of the essential oil on the skin bacteria and no inflammatory effects were observed under the allergy test. Conclusion: Zataria essential oil has antimicrobial effects on the skin infections in lower concentrations. The use of this essential oil as an antiseptic and preservative in cosmetics is recommended instead of chemical preservatives that generally have skin side effects.

SYNTHESIS, IN SILICO ANALYSIS AND ANTICONVULSANT ACTIVITY OF NOVEL PYRIMIDINE DERIVATIVES

INDIAN DRUGS ◽  
2021 ◽  
Vol 58 (05) ◽  
pp. 21-29
Author(s):  
Natasha N. Aggarwal ◽  
B. C. Revanasiddappa ◽  
Banylla Felicity ◽  
Vijay Kumar ◽  
Hemanth Kumar ◽  
...  
Keyword(s):  
In Silico ◽  
Anticonvulsant Activity ◽  
In Silico Analysis ◽  
Aromatic Aldehydes ◽  
Pyrimidine Derivatives ◽  
Mass Spectral ◽  
Seizure Models ◽  
Guanidine Carbonate ◽  
Silico Analysis

In this present study, a novel series of chalcones (C1-10) were synthesized by reacting 4-nitro acetophenone and various substituted aromatic aldehydes in an alcohol medium. The title compounds, pyrimidine derivatives (PD1-10), were obtained by the cyclization of chalcones (C1-10) with guanidine carbonate in an alcoholic medium. Each of the newly synthesized compounds was structurally assigned in accordance with FT-IR, 1 H-NMR and mass spectral data. All the synthesized compounds were subjected to in silico analysis among which, some of the synthesized compounds were chosen and evaluated for in vivo anticonvulsant study by employing PTZ-induced seizure and MES seizure models. Compounds PD2 and PD7 demonstrated significant anticonvulsant activity when compared to the standard.

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