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Deven See Lab

Graduate Students

Elliott Marston

Ph.D. Student, Plant Pathology

Interests: Genetics, discovering of genetic markers for marker assisted selection (MAS), biotic and abiotic stressors of wheat. Main project is focused on the identification of QTL’s and markers for MAS relating to late maturity alpha-amylase.

Esraa Alwan

 width=Ph.D. Student, Crop and Soil Sciences

Interests: Spring Wheat breeding, genetics, tissue culture/doubled haploids production, identifying new sources of resistance to wheat pathogens and insects. Main project is focused on identifying new sources of resistance to stripe rust and Hessian fly in the Pacific Northwest Spring Wheat germplasm.

Publications: Alwan, E., Ogbonnaya, F.C., Nazari, K., Hakim. Identification and characterization of wild tetraploids wheat for durable stem rust resistance. 2010.

Jonathan Eagle

Ph.D. Student, Plant Pathology

Interests: Plant-pathogen interactions, genetics, and plant breeding. My project pertains to a seedling stripe rust resistance in wheat which will involve gene mapping with SSR in hopes of finding new genes responsible for stripe rust resistance.

Sajal Sthapit

Ph.D. Student, Plant Pathology

Interests: Plant breeding and genetics, evolution, population genetics, bioinformatics, pre-breeding in neglected and underutilized species. My main project is to discover the genes that are associated with adaptation of wheat genotypes to the Washington state growing conditions.

Professional Experience: Senior Program Officer, LI-BIRD, Nepal, 2010-2015, now on study leave. URL: www.libird.org

Program Associate, EcoAgriculture Partners, Washington DC, 2007-2010. URL: www.ecoagriculture.org

Publications:
Palikhey, E., L. Sherpa, and S. Sthapit. 2015. From rarity to ubiquity: entrepreneurship revives rare rice variety. LEISA India June: 22-5
Shrestha, P. and S. Sthapit. 2015. Nepal: LI-BIRD’s approach to supporting community seed banks. In: Vernooy et al. eds. Community Seed Banks: Origins, Evolution and Prospects. Earthscan by Routledge, p. 187-93
Sthapit, S., G. Meldrum, S. Padulosi and N. Bergamini. 2015. Strengthening the role of custodian farmers in the national conservation programme of Nepal. Bioversity International and LI-BIRD
Mijatovic, D. and S. Sthapit. 2014. Conservation of agrobiodiversity in landscape mosaics, Nepal. ETFRN News 56, p. 88-93
Shrestha, P. and S. Sthapit. 2014. Conservation by communities: the CBM approach. LEISA India March: 11-3
Sthapit, S. and D. Mijatovic. 2014. The evolving landscape of agrobiodiversity conservation. LI-BIRD and Bioversity International
Happychuk, N., E. Palikhey, L. Lama, S. Sthapit and S. Shukla. 2014. Reacquiring a taste for diversity: changing food habits, their causal factors, and the value of dietary diversity in Jumla, Nepal. Biodiversity Watch 4: 167-97
Neupane, S., S. Sthapit and B. Sthapit. 2014. Following walnut footprints in Nepal. Scripta Horticulturae 17: 275-81
Paudel, B. and S. Sthapit. 2013. Empowering rights-holders and facilitating duty-bearers to secure farmers’ rights in Nepal. In: Jonas, H. and H. Jonas eds. The Right to Responsibility: Resisting and Engaging Development, Conservation, and the Law in Asia. p. 120-34
Shrestha, P., S. Sthapit, A. Subedi and B. Sthapit. 2013. Community biodiversity management fund: promoting conservation through livelihood development in Nepal. In: de Boef et al. eds. Community Biodiversity Management: Promoting Resilience and the Conservation of Plant Genetic Resources. Earthscan from Routledge, p. 118-22
Pudasaini, R., S. Sthapit, R. Suwal and B. Sthapit. 2013. Case study 2 – The role of integrated home gardens and local, neglected and underutilized plant species in food security in Nepal and meeting the Millennium Development Goal 1 (MDG). In: Fanzo et al. eds. Diversifying Food and Diets: Using Agricultural Biodiversity to Improve Nutrition and Health. Earthscan from Routledge, p. 242-56
Sthapit, B., V. Ramanatha Rao and S. Sthapit, eds. 2012. Tropical Fruit Tree Species and Climate Change. Bioversity International
Scherr, S.J. and S. Sthapi­t. 2009. Putting food on the table, crops and livestock. In: McNeely et al. eds. The Wealth of Nature: Ecosystem Services, Biodiversity, and Human Well-Being. Intl. League of Conservation Photographers, p. 219-26
Scherr, S.J. and S. Sthapit. 2009. Mitigating climate change through food and land use. Worldwatch Report 179
Scherr, S.J. and S. Sthapit. 2009. Farming and land use to cool the planet. In: Starke, L. ed. State of the World, p. 30-49


Visiting Scientists

Kanokporn Triwitayakorn (“Tik”)

Fulbright Visiting Scientist

Institute of Molecular Biosciences,

Mahidol University, Thailand

 

 


 

Staff

K. Marlowe (“Marlowe”)

USDA Research Technician

Education: Ph.D., Botany, Washington State University; B.S., Biology, Communications, University of Colorado
Expertise: Next-Generation sequencing, DNA extraction, PCR

Email: marlowe@wsu.edu

Travis Ruff

USDA Research Technician

Education: B.S., Biotechnology and Microbiology, Washington State University
Expertise: Next-Generation sequencing, PCR, Sanger sequencing

Email: truff@wsu.edu

Dolores Covarrubias

Research Technician

Education: B.S., Field Crops Management, Washington State University
Expertise: Next-Generation Sequencing, DNA Extraction, PCR, and SEQUENOM.

Email: dolores.covarrubias@wsu.edu


Computational Capacity

The See Lab as its computational capabilities required to handle large data sets generated by the in-house NGS platforms. We have a 32 core, 512GB RAM system for running the various computational jobs in the lab. In addition, there is a 96 core, 1TB RAM high performance computing cluster for massive parallel computation.

Servers

  • Supercomputer: WRSGGL01
    32 cores, 512GB RAM total memory
  • High Performance Computing Cluster: WRSGGLcluster
    4 compute nodes, 24 cores per node, 1TB RAM memory

Storage

  • Supercomputer
  • HPC
  • RAID storage connected to HPC
  • Independent RAID storage

Technologies, Equipment & Capabilities

Next-Gen Sequencing

  • Ion Proton (90 Million Reads/2.5 hours)
    -SNP variant calling (Genotyping by Sequencing or GBS)
    -RNA Sequencing
    -Whole genome sequencing
  • Ion Torrent (3 Million reads)
    -RNA seq(Transcriptome sequencing)
  • Illumina NextSeq®500
    -400 million reads/12hours
    -Exome Sequencing
    -Targeted Gene Sequencing (amplicon, gene panel)
    -Whole-Transcriptome Sequencing
    -Cytogenomic Arrays

Sanger Sequencing

  • ABI 3730

Fragment Analysis

  • SSR
  • STS
  • CAP

DNA Extraction

  • Bead Shaker
  • Oktopure
  • Synergy Microplate Reader (Quantification)
  • QiAgility

SNP Analysis

  • Sequenom
  • KASP
  • Synergy Microplate Reader

Software

  • GeneMarker (v1.5,v1.9) [Soft Genetics]
  • MassArray/Typer4.0.20 [Sequenom]
  • Gen5 2.0 [BioTek/Synergy Plate reader]
  • [QiAgility]
  • JMP Genomics
  • Multipoint
  • MultiQTL

Computational Resources

  • Supercomputer
    32 cores, 512GB RAM total
  • High Performance Computing Cluster: WRSGGLcluster
    4 compute nodes, 24 cores per node, 256 GB RAM per node
  • Storage devices

 


Undergraduates

Grace Murekatete Major: Agriculture Biotechnology
Emma McGinty Major: Botany

Former Members

  • Taras Nazarov, Ph.D. Plant Pathology
  • Jennifer Logan, Research Technician
  • Jinita Sthapit, Ph.D. Plant Pathology
  • Vandhana Krishnan, Associate in Research, Bioinformatician
  • Derick Jiwan, Post-Doctoral Researcher, Crop Sciences
  • Ian Harkins, Major: Environmental Engineering
  • Patrick McSweeney, Major: Computer Science