pankaj's blog

NSF recently awarded funding to the Planteome Project (http://www.planteome.org), an international collaboration to support the development of 'Common Reference Ontologies and Applications for Plant Biology' for a three year period. The Project will develop a set of common data standards and universal reference vocabularies to describe and standardized plant gene and phenotype annotation workflow

We have an immediate opening for a software and database developer to work on the NSF funded Planteome project (www.planteome.org). This open-source computational biology, comparative genomics, and bioinformatics project involves the development and maintenance of databases, software and automated data analysis pipelines. The incumbent will have a proven track record of database development in MySQL (with exposure to Solr, noSQL, and/or MongoDB) and experience developing software in Python, Perl, PHP, and Java.

Pathway database called Plant Reactome (http://plantreactome.gramene.org) has an immediate opening for a full-time biocurator to annotate plant metabolic, signaling and regulatory pathways. The successful candidate will be a recent PhD (within 0-5 years) in one or more areas of biochemistry, molecular biology, gene regulation, plant biology, epigenetics, bioinformatics, gene expression and related fields including the use of NGS technology. For more details visit http://aspb.site-ym.com/networking/apply_now.aspx?view=2&id=277576

Twelve students (9th-12th grade) from local schools attended DNA Biology Summer Camp organized by Jaiswal laboratory at Oregon State University in July 2014. The activities in the camp included short introductory lectures and follow up exercises using models and laboratory experiments. The learning in a collaborative environment was encouraged to further enrich their camp experience. Dr. Laurel Cooper, a research associate in the Jaiswal laboratory, introduced the students to the basics of the plant cell, and genetic material.

Source: OSU press release In a collaborative effort spanning five continents, scientists have announced the complete sequencing of one of the world's most widely planted trees, Eucalyptus grandis. Used for fuel and timber, the species commonly known as flooded gum or rose gum is valued for fast growth and straight grain. Often grown as a hybrid, it is one of more than 500 species of eucalyptus trees and shrubs that provide a renewable source of fiber, pulp, biofuel material, and medicinal and industrial oils. The accomplishment was published today in the scientific journal Nature.

Source: Department of Botany and Plant Pathology News Common bread wheat with a genome that is ~5 times the size of the human genome is a hexaploid, with three times more number of chromosomes compared to ancestral diploid genomes. This means that the bread wheat combines three different genomes and can make studying the genetic makeup of modern wheat difficult. Therefore, "studying ancestral genomes such as the wheat A, B and D genomes individually provide a baseline reference and new opportunities to investigate the genetic contribution of each of these genomes that lead to the development of bread wheat”. “It also gives us an opportunity to identify novel and beneficial stress tolerant genes in the wild ancestral genomes, that can be introduced into common bread wheat for improving varieties” added Jaiswal.

"Did you know that there are millions of DNA building blocks encoded in the genome of a plant? How can scientists possibly study this vast amount of data? With computers! Come and explore the tools of modern biology used to examine the complexities of DNA. This camp will involve hands-on activities where you will extract genetic material from a plant, assemble DNA sequences, identify genes using computers, examine your plant’s genome with visualization software, and test and look at your results in the laboratory. No programming skills required!"

Immediate opening is available for a recent PhD graduate (0-3 years after PhD award) to apply for a full-time postdoctoral scholar position. The biocuration would involve annotating plant metabolic, signaling and regulatory pathways for developing an online Plant Pathway database.

The genome of cyclosporine (synonym: cyclosporin) drug producing fungus Tolypocladium inflatum was published recently by Bushley et al. (2013), in the journal PLOS Genetics. The genome sequencing and its annotation discovered a cyclosporin biosynthesis associated metabolite gene cluster. "Cyclosporin is a powerful immunosupressant with a specific action on T-lymphocyte cells.

Nearly half of the world's population acquires their staple calories from rice. While the Green revolution has witnessed substantial increases in the production, availability and global per capita consumption of rice, FAO estimates 870 million of the world population to be still hungry. To increase production and especially to alleviate effect of climate change on rice production it is imperative that rice breeding moves beyond the Green Revolution and incorporate modern genomics based methods.