Not Available

Not AvailableInsect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client– server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn.Not Availabl

Not Available

Not AvailableInsect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client–server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn.Not Availabl

<i>In Silico</i> evaluation and identification of fungi capable of producing endo-inulinase enzyme

<div><p>The enzyme endo-inulinase hydrolyzes inulin to short chain fructooligosaccharides (FOS) that are potential prebiotics with many health promoting benefits. Although the raw materials for inulin production are inexpensive and readily available, commercial production of FOS from inulin is limited due to inadequate availability of the enzyme source. This study aimed to identify the fungi capable of producing endo-inulinase based on the <i>in silico</i> analysis of proteins retrieved from non-redundant protein sequence database. The endo-inulinase of <i>Aspergillus ficuum</i> was used as reference sequence. The amino acid sequences with >90% sequence coverage, belonging to different fungi were retrieved from the database and used for constructing three-dimensional (3D) protein models using SWISS-MODEL and Bagheerath H. The 3D models of comparable quality as that of the reference endo-inulinase were selected based on QMEAN Z score. The selected models were evaluated and validated for different structural and functional qualities using Pro-Q, ProSA, PSN-QA, VERIFY-3D, PROCHECK, PROTSAV metaserver, STRAP, molecular docking, and molecular dynamic simulation analyses. A total of 230 proteins belonging to 53 fungal species exhibited sequence coverage >90%. Sixty one protein sequences with >60% sequence identity were modeled as endo-inulinase with higher QMEAN Z Score. The evaluations and validations of these 61 selected models for different structural and functional qualities revealed that 60 models belonging to 22 fungal species exhibited native like structure and unique motifs and residues as that of the reference endo-inulinase. Further, these models also exhibited similar kind of interaction between the active site around the conserved glutamate residue and substrate as that of the reference endo-inulinase. In conclusion, based on the current study, 22 fungal species could be identified as endo-inulinase producer. Nevertheless, further biological assessment of their capability for producing endo-inulinase is imminent if they are to be used for commercial endo-inulinase production for application in FOS industry.</p></div

RMSD plot of protein backbone of 9 predicted endo-inulinase models and a reference endo-inulinase (3SC7) after 10ns of MD simulations.

<p>The data was generated using gromacs rms function. A. Protein back bone of enzyme-substrate complex; B. Protein backbone of enzyme without substrate. The plots were made in the work sheet.</p

Ramachandran plots of representative proteins that resembled as endo-inulinase.

<p>The plots were generated using PROCHECK module of PROTSAV webserver (<a href="http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp" target="_blank">http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp</a>).</p

Experimentally characterized endo-inulinases from species identified in this study.

<p>Experimentally characterized endo-inulinases from species identified in this study.</p

Three-dimensional (3D) model of representative fungal protein, constructed based on denovo/ab-initio method of protein modeling using Bhageerath H web server (http://www.scfbio-iitd.res.in/bhageerath/bhageerath_h.jsp).

<p>A- Reference endo-inulinase (3SC7); B- Denovo 3D model of predicted protein from <i>Aspergillus fumigatus</i> resembling native endo-inulinase like structure. The model images were created using USCF-Chimera.</p

Three-dimensional (3D) models of representative fungal proteins that resembled as endo-inulinase.

<p>3D models were generated from sequences retrieved from the non-redundant protein sequence database using SWISS-MODEL web server (<a href="https://swissmodel.expasy.org/interactive" target="_blank">https://swissmodel.expasy.org/interactive</a>). The model images were created using USCF-Chimera.</p

Comparative Transcriptome Analysis to Reveal Differentially Expressed Cytochrome P450 in Response to Imidacloprid in the Aphid Lion, <i>Chrysoperla zastrowi sillemi</i> (Esben-Petersen)

The aphid lion, Chrysoperla zastrowi sillemi (Neuroptera: Chrysopidae) is a highly effective beneficial predator of many agricultural pests and has developed resistance to several insecticides. Understanding the molecular mechanism of insecticide resistance in the predators is crucial for its effective application in IPM programs. Therefore, transcriptomes of imidacloprid-resistant and susceptible strains have been assessed using RNA-seq. Cytochrome P450 is one of the important gene families involved in xenobiotic metabolism. Hence, our study focused on the CYP gene family where mining, nomenclature, and phylogenetic analysis revealed a total of 95 unique CYP genes with considerable expansion in CYP3 and CYP4 clans. Further, differential gene expression (DGE) analysis revealed ten CYP genes from CYP3 and CYP4 clans to be differentially expressed, out of which nine genes (CYP4419A1, CYP4XK1, CYP4416A10, CYP4416A-fragment8, CYP6YL1, CYP6YH6, CYP9GK-fragment16, CYP9GN2, CYP9GK6) were downregulated and one (CYP9GK3) was upregulated in the resistant strain as compared to the susceptible strain. Expression validation by quantitative real-time PCR (qRT-PCR) is consistent with the DGE results. The expansion and differential expression of CYP genes may be an indicator of the capacity of the predator to detoxify a particular group of insecticides

The Interaction between the active site around the conserved glutamate residue and substrate (kestopentaose) in the three-dimensional protein models of reference endo-inulinase from <i>Aspergillus ficuum</i> and predicted endo-inulinase from <i>Talaromyces sp</i>.

<p>The docking was performed using MGL python tool and autodock 4. The interactions and hydrogen bonds formed between the substrate and the active site of enzyme was visualized using UCSF Chimera. The hydrogen bonds formed and their size were indicated in red color.</p