Enhancing microbiological safety of water and food

2014 ◽  
Author(s):  
◽  
Zhenyu Shen
Keyword(s):  
16S Rdna ◽  
In Silico ◽  
Mung Bean ◽  
Disease Outbreaks ◽  
Laboratory Strain ◽  
Human Pathogens ◽  
University Of Missouri ◽  
Enterohaemorrhagic Escherichia Coli ◽  
Wastewater Samples

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Human and animal feces are the main sources of pathogens associated with foodborne and waterborne disease outbreaks. The studies in Volume I proposed ribosomal intervening sequences (IVSs) can be used as host-specific genetic markers for tracking fecal sources in polluted food and water. In Chapter 3, using bioinformatics tools, one IVS in Faecalibacterium 16S rDNA specific to poultry (chicken and turkey) was identified in silico. A PCR assay was then developed to confirm the IVS was only present in fecal or wastewater samples from poultry. The study in Chapter 4 comprehensively examined host specificities of IVSs in 16S rDNA of 73 genera of fecal bacteria. A total of 13 IVSs were identified to be associated particular host sources in silico and the host-specificities of eight of them were confirmed by PCR reactions. Furthermore, a novel beef cattle-specific IVS was identified with next generation sequencing (NGS). Internalization of human pathogens in produce poses high risks to human health because the surface-sanitization method fail to inactivate the pathogens. The study in Volume II proposed to control the pathogen internalization with endophytic Bacillus subtilis strains isolated from vegetables. Twelve endophytic B. subtilis strains isolated from inner tissue of lettuce stems and mung bean seeds displayed inhibitory activity against a Salmonella enterica indicator in vitro and two of them (LCA1 and M24) showed broad inhibitory spectrums. LCA1, M24, and a laboratory strain B. subtilis 168 could internalize in mung bean sprouts and significantly reduced the internalization of S. enterica and enterohaemorrhagic Escherichia coli (EHEC).

scholarly journals Synthesis, Biological Assessment, and Structure Activity Relationship Studies of New Flavanones Embodying Chromene Moieties

Molecules ◽  
2020 ◽  
Vol 25 (3) ◽  
pp. 544 ◽  
Author(s):  
Eman Assirey ◽  
Azhaar Alsaggaf ◽  
Arshi Naqvi ◽  
Ziad Moussa ◽  
Rawda M. Okasha ◽  
...  
Keyword(s):  
In Silico ◽  
Biological Assessment ◽  
Diffusion Method ◽  
Breast Adenocarcinoma ◽  
Cytotoxic Activities ◽  
Human Pathogens ◽  
Bacterial Strains ◽  
Human Carcinoma ◽  
In Silico Studies

Novel flavanones that incorporate chromene motifs are synthesized via a one-step multicomponent reaction. The structures of the new chromenes are elucidated by using IR, 1H-NMR, 13C-NMR, 1H-1H COSY, HSQC, HMBC, and elemental analysis. The new compounds are screened for their in vitro antimicrobial and cytotoxic activities. The antimicrobial properties are investigated and established against seven human pathogens, employing the agar well diffusion method and the minimum inhibitory concentrations. A majority of the assessed derivatives are found to exhibit significant antimicrobial activities against most bacterial strains, in comparison to standard reference drugs. Moreover, their cytotoxicity is appraised against four different human carcinoma cell lines: human colon carcinoma (HCT-116), human hepatocellular carcinoma (HepG-2), human breast adenocarcinoma (MCF-7), and adenocarcinoma human alveolar basal epithelial cell (A-549). All the desired compounds are subjected to in-silico studies, forecasting their drug likeness, bioactivity, and the absorption, distribution, metabolism, and excretion (ADME) properties prior to their synthetic assembly. The in-silico molecular docking evaluation of all the targeted derivatives is undertaken on gyrase B and the cyclin-dependent kinase. The in-silico predicted outcomes were endorsed by the in vitro studies.

scholarly journals Molecular Modeling and Structural Stability of Wild-Type and Mutant CYP51 from Leishmania major: In Vitro and In Silico Analysis of a Laboratory Strain

Molecules ◽  
2018 ◽  
Vol 23 (3) ◽  
pp. 696 ◽  
Author(s):  
Masoud Keighobadi ◽  
Saeed Emami ◽  
Milad Lagzian ◽  
Mahdi Fakhar ◽  
Alireza Rafiei ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Structural Stability ◽  
In Silico ◽  
Leishmania Major ◽  
In Silico Analysis ◽  
Laboratory Strain ◽  
Wild Type ◽  
Silico Analysis

scholarly journals Universal microbial diagnostics using random DNA probes

2016 ◽  
Vol 2 (9) ◽  
pp. e1600025 ◽  
Author(s):  
Amirali Aghazadeh ◽  
Adam Y. Lin ◽  
Mona A. Sheikh ◽  
Allen L. Chen ◽  
Lisa M. Atkins ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Pathogenic Bacteria ◽  
Disease Outbreaks ◽  
Dna Probes ◽  
Signal Recovery ◽  
Human Pathogens ◽  
Infectious Disease Outbreaks ◽  
Target Dna ◽  
Detection Schemes

Early identification of pathogens is essential for limiting development of therapy-resistant pathogens and mitigating infectious disease outbreaks. Most bacterial detection schemes use target-specific probes to differentiate pathogen species, creating time and cost inefficiencies in identifying newly discovered organisms. We present a novel universal microbial diagnostics (UMD) platform to screen for microbial organisms in an infectious sample, using a small number of random DNA probes that are agnostic to the target DNA sequences. Our platform leverages the theory of sparse signal recovery (compressive sensing) to identify the composition of a microbial sample that potentially contains novel or mutant species. We validated the UMD platform in vitro using five random probes to recover 11 pathogenic bacteria. We further demonstrated in silico that UMD can be generalized to screen for common human pathogens in different taxonomy levels. UMD’s unorthodox sensing approach opens the door to more efficient and universal molecular diagnostics.

scholarly journals In Vitro and In Silico Approaches for the Evaluation of Antimicrobial Activity, Time-Kill Kinetics, and Anti-Biofilm Potential of Thymoquinone (2-Methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione) against Selected Human Pathogens

Antibiotics ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 79
Author(s):  
Kamal A. Qureshi ◽  
Mahrukh Imtiaz ◽  
Adil Parvez ◽  
Pankaj K. Rai ◽  
Mariusz Jaremko ◽  
...  
Keyword(s):  
Candida Albicans ◽  
In Silico ◽  
Xylose Reductase ◽  
Human Pathogens ◽  
Target Proteins ◽  
Antimicrobial Potential ◽  
Antibacterial And Antifungal ◽  
In Silico Molecular Docking ◽  
Time Kill

Thymoquinone (2-methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione; TQ), a principal bioactive phytoconstituent of Nigella sativa essential oil, has been reported to have high antimicrobial potential. Thus, the current study evaluated TQ’s antimicrobial potential against a range of selected human pathogens using in vitro assays, including time-kill kinetics and anti-biofilm activity. In silico molecular docking of TQ against several antimicrobial target proteins and a detailed intermolecular interaction analysis was performed, including binding energies and docking feasibility. Of the tested bacteria and fungi, S. epidermidis ATCC 12228 and Candida albicans ATCC 10231 were the most susceptible to TQ, with 50.3 ± 0.3 mm and 21.1 ± 0.1 mm zones of inhibition, respectively. Minimum inhibitory concentration (MIC) values of TQ are in the range of 12.5–50 µg/mL, while minimum biocidal concentration (MBC) values are in the range of 25–100 µg/mL against the tested organisms. Time-kill kinetics of TQ revealed that the killing time for the tested bacteria is in the range of 1–6 h with the MBC of TQ. Anti-biofilm activity results demonstrate that the minimum biofilm inhibitory concentration (MBIC) values of TQ are in the range of 25–50 µg/mL, while the minimum biofilm eradication concentration (MBEC) values are in the range of 25–100 µg/mL, for the tested bacteria. In silico molecular docking studies revealed four preferred antibacterial and antifungal target proteins for TQ: D-alanyl-D-alanine synthetase (Ddl) from Thermus thermophilus, transcriptional regulator qacR from Staphylococcus aureus, N-myristoyltransferase from Candida albicans, and NADPH-dependent D-xylose reductase from Candida tenuis. In contrast, the nitroreductase family protein from Bacillus cereus and spore coat polysaccharide biosynthesis protein from Bacillus subtilis and UDP-N-acetylglucosamine pyrophosphorylase from Aspergillus fumigatus are the least preferred antibacterial and antifungal target proteins for TQ, respectively. Molecular dynamics (MD) simulations revealed that TQ could bind to all four target proteins, with Ddl and NADPH-dependent D-xylose reductase being the most efficient. Our findings corroborate TQ’s high antimicrobial potential, suggesting it may be a promising drug candidate for multi-drug resistant (MDR) pathogens, notably Gram-positive bacteria and Candida albicans.

scholarly journals In Silico Screening and In Vitro Assessment of Natural Products with Anti-Virulence Activity against Helicobacter pylori

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 20
Author(s):  
Maciej Spiegel ◽  
Paweł Krzyżek ◽  
Ewa Dworniczek ◽  
Ryszard Adamski ◽  
Zbigniew Sroka
Keyword(s):  
Helicobacter Pylori ◽  
In Silico ◽  
Stringent Response ◽  
Human Pathogens ◽  
Gastric Diseases ◽  
Natural Substances ◽  
Interesting Candidate ◽  
H Pylori ◽  
Static Conditions

Helicobacter pylori is one of the most frequent human pathogens and a leading etiological agent of various gastric diseases. As stringent response, coordinated by a SpoT protein, seems to be crucial for the survivability of H. pylori, the main goal of this article was to use in silico computational studies to find phytochemical compounds capable of binding to the active site of SpoT from H. pylori and confirm the ability of the most active candidates to interfere with the virulence of this bacterium through in vitro experiments. From 791 natural substances submitted for the virtual screening procedure, 10 were chosen and followed for further in vitro examinations. Among these, dioscin showed the most interesting parameters (the lowest MIC, the highest anti-biofilm activity in static conditions, and a relatively low stimulation of morphological transition into coccoids). Therefore, in the last part, we extended the research with a number of further experiments and observed the ability of dioscin to significantly reduce the formation of H. pylori biofilm under Bioflux-generated flow conditions and its capacity for additive enhancement of the antibacterial activity of all three commonly used antibiotics (clarithromycin, metronidazole, and levofloxacin). Based on these results, we suggest that dioscin may be an interesting candidate for new therapies targeting H. pylori survivability and virulence.

In-vitro and In-silico analysisof anti-diabetic and anti-microbial activity of Cichorium intybus leaf extracts

2020 ◽  
Vol 16 ◽  
Author(s):  
Suganya Ramakrishnamurthy ◽  
Ganesan Singaravelu ◽  
Velmurugan Devadasan ◽  
Aruna Prakasarao
Keyword(s):  
In Silico ◽  
Ethanolic Extract ◽  
Ethanol Extract ◽  
Docking Studies ◽  
Human Pathogens ◽  
Leaf Extracts ◽  
Ligand Complex ◽  
Dynamic Simulations ◽  
In Silico Studies

Objective: To screen the selected phytochemicals against diabetes by docking studies in comparison with experimental analysis. Methods: Ethanol crude extract has been obtained from the leaves of C.intybus and its chemical compounds were identified using GC- MS. Docking studies were carried out for selected phytochemicals to find the binding affinity and H-bond interaction using Scrodinger suite. Dynamic simulations were carried out for protein ligand complex up to 50ns using desmond OPLS AA forcefield and α- Amylase and α- Glucosidase assay were carried for ethanolic extract to infer its inhibition. Results: Four compounds were chosen for induced fit docking based on the docking score and glide energy obtained from GLIDE-XP docking. The compounds were docked with the protein target human aldose reductase (PDB ID: 2FZD) for checking the anti-diabetic nature. The molecular dynamics simulations were carried out for the most favorable compounds and stability has been checked during the simulations. The ethanol extract exhibits significant α-amylase and α-glucosidase inhibitory activities with an IC50 value of 38µg and 88µg dry extract respectively and well compared with standard acarbose drug.The antimicrobial activity was also carried out for various extracts (Chloroform, Ethyl acetate and Ethanol) of the same (C. intybus) was screened against four selected human pathogens. Compared to other solvent extracts, ethanol and chloroform extract shows better inhibition and their minimal inhibitory concentration (MIC) value has been calculated. Conclusion: In-silico studies and in-vitro studies reveals that C.intybus plant compounds have more potent for treating diabetes

scholarly journals In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens

2021 ◽  
Vol 9 (11) ◽  
pp. 2297
Author(s):  
Sami Khabthani ◽  
Jean-Marc Rolain ◽  
Vicky Merhej
Keyword(s):  
In Silico ◽  
High Throughput Sequencing ◽  
Human Pathogens ◽  
Nonribosomal Peptide ◽  
Culture Techniques ◽  
Antimicrobial Substances ◽  
Potential Source ◽  
Antibiotic Compounds ◽  
Antibiotic Discovery

Antibiotics are majorly important molecules for human health. Following the golden age of antibiotic discovery, a period of decline ensued, characterised by the rediscovery of the same molecules. At the same time, new culture techniques and high-throughput sequencing enabled the discovery of new microorganisms that represent a potential source of interesting new antimicrobial substances to explore. The aim of this review is to present recently discovered nonribosomal peptide (NRP) and polyketide (PK) molecules with antimicrobial activity against human pathogens. We highlight the different in silico/in vitro strategies and approaches that led to their discovery. As a result of technological progress and a better understanding of the NRP and PK synthesis mechanisms, these new antibiotic compounds provide an additional option in human medical treatment and a potential way out of the impasse of antibiotic resistance.

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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