Organization: NAFA-Animal Production and Health Laboratory
Primary Location: Austria-Lower Austria-Seibersdorf-IAEA Laboratories in Seibersdorf
Job Posting: 2020-07-23, 7:44:53 PM
Closing Date: 2020-08-14, 6:59:00 AM
Duration in Months: 12
Contract Type: Special Service Agreement - SSA
The Department of Nuclear Sciences and Applications implements the IAEA's Major Programme 2, "Nuclear Techniques for Development and Environmental Protection". This Major Programme comprises individual programmes on food and agriculture, human health, water resources, environment and radiation technologies. These programmes are supported by laboratories in Seibersdorf, Monaco and Vienna. The Major Programme's objective is to enhance the capacity of Member States to meet basic human needs and to assess and manage the marine and terrestrial environments through the use of nuclear and isotopic techniques in sustainable development programmes.
The Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture assists Member States of the Food and Agriculture Organization of the United Nations (FAO) and the IAEA in using nuclear techniques and related technologies to improve food security, alleviate poverty and promote sustainable agriculture. The Joint Division consists of five Sections, each with an associated laboratory (located in Seibersdorf, 45 km south-east of Vienna), in the areas of: animal production and health; plant breeding and genetics; insect pest control; soil and water management and crop nutrition; and food and environmental protection.
The Animal Production and Health Section and Laboratory assist Member States in improving livestock productivity through the efficient use of locally available feed resources, reproduction and breeding practices, and disease diagnostic tools and control measures.
The Animal Production and Health Laboratory (APHL) of the Joint FAO/IAEA Division is carrying out the research and development of nuclear- and nuclear-related tools for the detection and surveillance of zoonotic diseases at the animal/human interface, to support disease control and surveillance programs.
As preparedness is critical for successful control of zoonotic and emerging viruses, and to avoid their spread in animals and humans, the APHL is focusing on the use of metagenomics and high throughput genomics methods to identify potential reservoir of zoonotic pathogens and discover new variants. Metagenomics is a powerful approach for the broad identification of pathogens in clinical samples, though data analysis is challenging.
As part of these activities, the laboratory is working on the creation and optimization of novel procedures for the direct identification of pathogens directly in clinical/environmental material using metagenomics and targeted sequencing approaches.
The consultant shall work at the intersection of bioinformatics and metagenomics. S/he will actively work in the laboratory to process samples for genetic analysis using the Ion S5 sequencing and Oxford Nanopore's MinION technologies to generate data as well as on bioinformatic platforms to analyse the genetic data obtained. The aim is to develop, test, and apply innovative metagenomics approaches, compatible with friendly and consistent bioinformatics analysis pipelines, for the direct detection of viruses in clinical samples. In close collaboration with the laboratory team, the molecular biologist will take part in the development and optimization of innovative metagenomic approaches for pathogens' detection and discovery.
Functions / Key Results expected
The incumbent shall work in collaboration and in close communication with the APHL Research and Development (R&D) team to:
- Develop and validate a metagenomics approach to identify bacterial and viral agents in clinical samples,
- Undertake data analysis of genomics and transcriptomics projects.
- Expand the utility and application of high-throughput and metagenomics to the direct detection of pathogens in clinical samples collected from animals (both production animals and wildlife).
- Establish a proof of concept and demonstrate the feasibility and potential value of novel diagnostic approaches for the viral surveillance.
- Prepare protocols and assist in developing automated computational pipelines for data analysis
- Prepare and present the results for scientific publications and to audience not familiar with genomics.
- Prepare teaching materials and SOPs for the dissemination to member states' laboratories.
Knowledge, Skills and Abilities
- Natural Sciences
- Animal Diseases
Qualifications and Experience
- Doctorate Degree - related to (human and/or animal) infectious diseases, pathogens discovery and genetic analysis and University degree Biological sciences, biomedical sciences, veterinary sciences or a closely related field
- Solid knowledge of animal or human viruses and assay development;
- Strong background in molecular biology techniques including molecular cloning, PCR (Polymerase Chain Reaction)/qPCR (Quantitative Polymerase Chain Reaction) and library preparation for next-generation sequencing;
- Experience in R programming or other statistical software;
- Experience with UNIX computer systems;
- Understanding of genome alignment, mapping, variant calling, and annotation
- Understanding of molecular phylogeny and evolution
- Familiarity with public sequence databases
- Ability and enthusiasm for working collaboratively in a multidisciplinary and multicultural environment;
- Good communication skills;
- Excellent publication records in the related fields;
- Ability to manage time and meet deadlines;
- Self-driven with keen attention to detail and documentation
- Excellent oral and written command of English. Knowledge of other official IAEA languages (Arabic, Chinese, French, German, Russian and Spanish) is an asset.
The remuneration for this consultancy is a daily fee of up to a maximum of € 238,09, based on qualifications and experience. In case duty travel is required within the assignment, a daily subsistence allowance (DSA) and travel costs are provided. Health coverage and pension fund are the responsibility of the incumbent.