Analysis of the Barley Malt Rootlet Proteome

Barley seeds are one of the main ingredients of the malting industry for brewing beer. The barley rootlets that are separated from the kilned seeds at the end of the malting process and used as animal feed are one of the byproducts of this industry. In this study, the proteome of rootlets derived from two stages of the malting process, germination and kilning, from a popular malting barley variety were analyzed. A label-free shotgun proteomics strategy was used to identify more than 800 proteins from the barley rootlets. A high coverage and high confidence Gene Ontology annotations of the barley genome was used to facilitate the functional annotation of the proteins that were identified in the rootlets. An analysis of these proteins using Kellogg Encyclopedia of Genes and Genomes (KEGG) and Plant Reactome databases indicated the enrichment of pathways associated with phytohormones, protein biosynthesis, secondary metabolism, and antioxidants. Increased levels of jasmonic acid and auxin in the rootlets further supported the in silico analysis. As a rich source of proteins and amino acids use of these by-products of the malting industry for animal feed is validated. This study also indicates rootlets as a potential source of naturally occurring phenylpropanoids and antioxidants that can be further exploited in the development of functional foods.

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In silico Analysis of Phytochemicals from Glycyrrhiza glabra against Conjunctivitis

European Journal of Medicinal Plants ◽

10.9734/ejmp/2020/v31i530236 ◽

2020 ◽

pp. 11-16

Author(s):

Shibani Sahoo ◽

Swetanginee Gouda ◽

Sunanya Das ◽

Mukundjee Pandey ◽

Dipankar Bhattacharyay

Keyword(s):

Plant Extract ◽

In Silico Analysis ◽

Glycyrrhiza Glabra ◽

Biologically Active ◽

Positive Bacterium ◽

Discovery Studio ◽

Plant Parts ◽

Naturally Occurring ◽

Dehydrogenase Enzyme ◽

Silico Analysis

Phytochemicals are naturally occurring biologically active compounds found in plant parts such as roots, barks, leaves, seeds, and even pulps. It has been reported that Glycyrrhiza glabra plant extract is used for treatment of the disease conjunctivitis. The plant extract contains different phytochemicals. The agent that causes conjunctivitis is a gram positive bacterium which belongs to species Staphylococcus. One of the key enzymes involved in its biochemical pathway is Isocitrate dehydrogenase. The molecular docking of the phytochemicals with the enzyme was studied using Biovia Discovery Studio. The strength of the interaction was evaluated based on -CDocker energy and -CDocker interaction energy. High positive values for both the parameters indicated that out of different phytochemicals rosmarinic acid can effectively deactivate the is ocitrate dehydrogenase enzyme thereby inhibiting the life cycle of Staphylococcus.

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Cis-2 and trans-2-eisocenoic fatty acids are novel inhibitors for Mycobacterium tuberculosis Protein tyrosine phosphatase A

Acta Biochimica Polonica ◽

10.18388/abp.2020_5201 ◽

2020 ◽

Author(s):

Lalu Rudyat Telly Savalas ◽

Baiq Repika Nurul Furqon ◽

Dina Asnawati ◽

Jannatin 'Ardhuha ◽

Prapti Sedijani ◽

...

Keyword(s):

Fatty Acids ◽

Mycobacterium Tuberculosis ◽

Protein Tyrosine Phosphatase ◽

Tyrosine Phosphatase ◽

Latent Tuberculosis ◽

In Silico Analysis ◽

Eicosenoic Acid ◽

Protein Tyrosine ◽

Naturally Occurring ◽

Silico Analysis

Small protein tyrosine phosphatase (PtpA) of Mycobacterium tuberculosis is attributed to the development of latent tuberculosis infection, and hence bocomes an interesting target for drug development. In this communication, inhibition of PtpA by naturally occurring fatty acids cis-2 and trans-2-eicosenoic acid is investigated. Mtb PtpA was heterologously expressed in Escherichia coli, and the activity of PtpA was inhibited by cis-2 and trans-2 eicosenoic fatty acids. Both compunds showed strong inhibition of PtpA activity with IC50 at low micromolar concentration. As comparison, trans-11-eicosenoic acid only slightly inhibit PtpA. In silico analysis confirmed the inhibition of PtpB by cis-2-eicosenoic acid by formation of several hydrogen bonds. These findings show that cis-2 and trans-2 eicosenoic fatty acids are potential candidates for latent tuberculosis inhibitors.

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Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele

Molecular Immunology ◽

10.1016/j.molimm.2011.03.019 ◽

2011 ◽

Vol 48 (12-13) ◽

pp. 1461-1467 ◽

Cited By ~ 14

Author(s):

Dinler A. Antunes ◽

Maurício M. Rigo ◽

Jader P. Silva ◽

Samuel P. Cibulski ◽

Marialva Sinigaglia ◽

...

Keyword(s):

In Silico ◽

In Silico Analysis ◽

Naturally Occurring ◽

Silico Analysis

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A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

Seminars in Oncology ◽

10.1053/j.seminoncol.2020.02.012 ◽

2020 ◽

Vol 47 (6) ◽

pp. 398-408

Author(s):

Sonam Tulsyan ◽

Showket Hussain ◽

Balraj Mittal ◽

Sundeep Singh Saluja ◽

Pranay Tanwar ◽

...

Keyword(s):

Systematic Review ◽

Gallbladder Carcinoma ◽

In Silico ◽

In Silico Analysis ◽

Transcriptomic Profile ◽

Silico Analysis

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In Silico Analysis of Single Nucleotide Polymorphism in Human Prothrombin Gene

10.1055/s-0039-1680245 ◽

2019 ◽

Author(s):

I. Farah ◽

A. El-Mubark ◽

M. Osman ◽

A. Soliman ◽

F. Ali ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

In Silico ◽

In Silico Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Prothrombin Gene ◽

Silico Analysis

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Enalos Suite of Tools: Enhancing Cheminformatics and Nanoinfor - matics through KNIME

Current Medicinal Chemistry ◽

10.2174/0929867327666200727114410 ◽

2020 ◽

Vol 27 (38) ◽

pp. 6523-6535 ◽

Cited By ~ 3

Author(s):

Antreas Afantitis ◽

Andreas Tsoumanis ◽

Georgia Melagraki

Keyword(s):

Data Analysis ◽

Virtual Screening ◽

In Silico ◽

Model Development ◽

In Silico Analysis ◽

Material Design ◽

Efficient Solutions ◽

Biological Data ◽

Cost Efficient ◽

Silico Analysis

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we have developed the necessary tools to facilitate a variety of important tasks to construct workflows that will simplify the handling, processing and modeling of cheminformatics data and will provide time and cost efficient solutions, reproducible and easier to maintain. We therefore develop and present a toolbox of >25 processing modules, Enalos+ nodes, that provide very useful operations within KNIME platform for users interested in the nanoinformatics and cheminformatics analysis of chemical and biological data. With a user-friendly interface, Enalos+ Nodes provide a broad range of important functionalities including data mining and retrieval from large available databases and tools for robust and predictive model development and validation. Enalos+ Nodes are available through KNIME as add-ins and offer valuable tools for extracting useful information and analyzing experimental and virtual screening results in a chem- or nano- informatics framework. On top of that, in an effort to: (i) allow big data analysis through Enalos+ KNIME nodes, (ii) accelerate time demanding computations performed within Enalos+ KNIME nodes and (iii) propose new time and cost efficient nodes integrated within Enalos+ toolbox we have investigated and verified the advantage of GPU calculations within the Enalos+ nodes. Demonstration data sets, tutorial and educational videos allow the user to easily apprehend the functions of the nodes that can be applied for in silico analysis of data.

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