Nutrient Use Efficiency (NtUE) Web-Resource




  • Conceived By : Chaudhary Charan Singh University Meerut
  • Supported By : Bioclues Organization , Osmania University , Uttarakhand Council For Biotechnology , BioBits Dehradun

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"Alien Species"
Wild Eienkorn
(Triticum urartu)
Tausch's Goatgrass
(Aegilops tauschii)
"Model Species
Purple False Brome
(Brachypodium distachyon)
Thale Cress
(Arabidopsis thaliana)
"Major cereal Crops"
Wheat (Triticum aestivum)Rice (Oryza sativa)Maize (Zea mays)Barley (Hordeum vulgare)


About Web-Resource

Cereals are the key contributors to global food security. Genes involved in uptake (transport), assimilation and utilization of macro- and micro-nutrients are responsible for their concentrations in grain and straw. Although many cereal genomic databases are available, currently there is no cohesive web-resource of manually curated nutrient use efficiency (NtUE) related genes and QTLs, etc. Here, we present a web-resource containing information on NtUE related genes/QTLs and the corresponding available microRNAs for some of these genes in three major cereal crops [wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays)], two alien species (Triticum urartu and Aegilops tauschii) related to wheat, and two model species including Brachypodium distachyon and Arabidopsis thaliana. Gene annotations integrated in the current web-resource were collected from the existing databases and the available literature. The primary goal of developing this web-resource is to provide descriptions of the NtUE related genes and their functional annotation. MicroRNA targeting some of the NtUE related genes and the quantitative trait loci (QTLs) for NtUE related traits are also included. The available information in the web-resource should help the users to readily search the desired information.







Team

Anuj Sharma, MSc

Bioinformatician
Uttarakhand Council for Biotechnology Dehradun
anunbioinfo91@gmail.com


Ajay Pandeya, B.Tech,(M.Tech)


Graphic Era University ,Dehradun
writetoajaypandeya@gmail.com


Girik Malik(B.Tech)

Shiv Nadar University, Noida (INDIA).
Visiting researcher, Ohio State University, USA
girik@bioclues.org


Vijay Gahlaut, MSc, PhD

Research Associate
Ch. Charan Singh University, Meerut
zone4vijay@gmail.com


Hima Kumari, MSc, PhD

Postdoctoral Fellow
Osmania University, Hyderabad (INDIA)
hima@bioclues.org


Anil Kumar, MSc, PhD

Postdoctoral Fellow
Osmania University, Hyderabad (INDIA)
anilkumarou@gmail.com


MNV Prasad Gajula,MCA, MS(Sweden), PhD(Germany)

Research Scientist (Bioinformatics)
DST Ramanujan Fellow
Institute of Biotechnology PJTSAU, Rajendra Nagar, Hyderabad-500030 INDIA
gajula.ibt@gmail.co


Prashanth N Suravajhala, PhD

Bioclues.org
Scientist, Birla Institute of Scientific Research, Jaipur
prash@bioclues.org


K. P. Singh, PhD
Professor and Vice-Chancellor

CCS Haryana Agricultural University Hisar - 125 004, India

vc@hau.ernet.in, kps_biophysics@yahoo.co.in


HS Balyan, PhD, FNASc, FNAAS, FNA

Hony. Emeritus Professor & INSA Senior Scientist
Ch. Charan Singh University, Meerut
hsbalyan@gmail.com


PB Kavi Kishor, PhD

Hony. CSIR Emeritus Professor
Osmania University, Hyderabad (INDIA)
pbkavi@yahoo.com


PK Gupta, PhD, FNASc, FNAAS, FASc, FNA

Hony. Emeritus Professor & INSA Senior Scientist
Ch. Charan Singh University, Meerut
pkgupta36@gmail.com

FAQs

1. What is NtUE web-resource?
Ans : Nutrient Use Efficiency web-resource is a repository of manually annotated genes, gene functions, related miRNAs and QTLs for NtUE related traits in important cereals with two alien species and two model species.

2. How many records do exist in NtUE?
Ans : As of June, 2016., the web-resource contains 688 records related to information on macro and micronutrients.

3. Why NtUE? Ain't any other database?
Ans : There is a dearth of nutrient use efficiency records from cereals. With no database available containing information about genes, microRNA and QTLs in cereals for NtUE related genes, we believe this resource serves as a compendium for functional annotation of NtUE related genes, microRNA and QTLs across important cereal crops.

4. How can we contribute to this project?
Ans : If you have a list of known/ unknown records related to NtUE, please contact Hony. Prof. Emeritus & INSA Senior Scientist PK Gupta and Hony. Prof. Emeritus & INSA Senior Scientist HS Balyan. They can be reached at pkgupta36@gmail.com and hsbalyan@gmail.com.

5. How can I query and use NtUE database?
Ans : You can search genes/QTLs/miRNAs against specific list of organisms enlisted. A wide gamut of tools and their APIs are being embedded to make this an effective webserver.

6. Can I download the entire web-resource?
Ans : You may request the authors by sending a requisition on why and how you are going to use it.

7. When and how can I find the web-resource updated?
Ans : Please join the mailing list at bioclues@googlegroups.com.

8. If our accession is already submitted in GenBank, can I find the record linked to NtUE web-resource?
Ans : We are trying to impart NCBI Linkout now. With NCBI Linkout, the queried sequences would have a direct reference to the records in the reference databases.

9. When I query a record of my interest, I get normalization/SQL error. Please help.

Ans : Please ensure that your port settings are open for: 8080. You may mail us for any queries, you have.

10. Is there an Application Program Interface (API) for the web-resource? This will allow us to link it to our webserver?
Ans : Yes, the web-resource is currently a beta version. We will have an API of it for you to host it internally.

11. Why is it that when I query K related genes, I get some unrelated NtUE hits?
Ans : It could be because the same NtUE record is linked to it.

12. Is NtUE web-resource compliant with Minimum Information for Bioinformatics Investigation (MIABI) standards?
Ans : Yes please. We are working on it. The converse may not be possible until the web-resource lapses the beta version.