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 Uma Aryal

Research Scientist
(765) 494-0716

Hi, my name is Uma Aryal. I joined Department of Biochemistry, Purdue University in May 2012 as a Research Scientist and I work with Drs. Mark Hall (Biochemistry), and Dan Szymanski (Agronomy).
Before moving to Purdue, I was a postdoctoral researcher at Pacific Northwest National Laboratory (PNNL) in the lab of Dr. Dick Smith. My research has focused on developing analytical methods for mass spectrometry (MS)-based quantitative proteomics, including the study of post-translational modifications (particularly phosphorylation and glycosylation), and identification and localization of protein complexes. For more than six years, I have applied these techniques to environmental, bio-energy and biomedical research problems using a variety of biological systems including filamentous fungi, plants, photosynthetic cyanobacteria and human and mouse plasma samples. My research training provided expertise with different analytical and bioinformatic approaches for MS-based proteomics including cell fractionation, affinity and immunoaffinity protein purification, metabolic labeling (e.g. SILAC), and analysis/interpretation of large-scale proteomics data using bioinformatics tools. For example, I developed a novel dynamic SILAC approach for real-time monitoring of new protein synthesis in cyanobacteria of the genus Cyanothece, and also worked on secretome and sub-cellular proteome analysis of the industrially important filamentous fungus Aspergillus niger.
Currently, at Purdue, I am helping lead an NSF funded research project which aims to discover and localize protein complexes in plants using multi-dimensional chromatography and quantitative MS.

Quantitative proteomics and posttranslational modification
1.  Aryal, U.K., Callister, S.J., Mishra, S., Zhang, X., Min, H., Shuttanandan, J.I., Koppenaal, D.W., Smith, R.D., Pakrasi, H.B. and Sherman, L.A. (2012). Proteome analyses of diazotrophic cyanobacteria Cyanothece ATCC51142 and PCC 7822 production in Cyanothece ATCC51142 and PCC7822 under culture conditions of enhanced H2-production. Applied and Environmental Microbiology, doi:10.1128/AEM.02254-12.
2.  Angel, T.E., Aryal, U.K., Hengel, S., Baker, E.S., Kelly, R.T., Robinson, E.R, and Smith, R.D. (2012). Mass spectrometry based proteomics: existing capabilities and future directions. Chemical Society Review, DOI: 10.1039/C2CS15331A (invited review).
3.  Aryal, U.K., Lin, C.T., Wang, L., Wang, J., Qian, W.J., and Lin, Y. (2012). Identification of butyrylcholinesterase in human plasma using immunoaffinity purification and mass spectrometry. Analytica Chemica Acta, 723:68-75.
4.   Aryal, U.K.*, Krochko, J.E. and Ross, A.R.S. (2012). Identification of phosphoproteins in Arabidopsis thaliana leaves using polyethylene glycol fractionation, immobilized metal-ion affinity chromatography, two-dimensional gel electrophoresis and mass spectrometry. Journal of Proteome Research, 11(1): 425-437 (*corresponding author).
5.    Aryal, U.K. Stockel, J., Welsh, E.A., Gritsenko, M.A., Nicora, C.D., Koppenaal, D.W., Smith, R.D., Pakrasi, H.B., Jacobs, J.M. (2012). Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light conditions. Journal of Proteome Research, 11(2): 609-619. 
Features in Biological Science Division research highlights:
6.  Wang, L., Aryal, U.K., Dai, Z., Mason, A.C.,  Tian, Z.X., Zhou, J.Y., Su, D., Weitz, K.K., Liu, T., Camp, D.G. II, Smith, R.D., Baker, S.E., and Qian, W.J. (2012). Mapping N-linked glycosylation sites in the secretome and whole cells of Aspergillus niger using hydrazide chemistry and mass spectrometry. Journal of Proteome Research, 11: 143-156.
7.  Aryal, U.K., Stöckel, J., Gritsenko, M.A., Krowvidi, R. Monroe, M.E., Koppenaal, D.W., Smith, R.D., Pakrasi, H.B., and Jacobs, J.M. (2011). Temporal and quantitative profiling of proteomics dynamics in a unicellular cyanobacterium Cyanothece ATCC51142. BMC Systems Biology, 5:194.
8. Aryal, U.K.* and Ross, A.R.S. (2010). Enrichment and analysis of phosphopeptides under different experimental conditions using titanium dioxide affinity chromatography and mass spectrometry. Rapid Communication in Mass Spectrometry, 24(2): 219-231. 
(* corresponding author)
One of the hottest 2010 articles in Analytical Science by WILEY-VCH:
9.  Aryal*, U.K., Olson, D.J.H., and Ross, A.R.S. (2008). Optimization of immobilized gallium (III) ion affinity chromatography for selective binding and recovery of phosphopeptides from protein digests. Journal of Biomolecular Techniques, 19(5): 296-310. (* corresponding author)
Soil microbiology and plant-microbe interaction
10.  Aryal, U.K., Shah, S.K., and Xu, H.L. (2007). Mycorrhizae and dryland agriculture: Drought resistance and water use efficiency of mycorrhizal plants. In H.L. Xu (ed.), Dryland Crop Production -Technology Breakthrough and Study Cases. Research Signpost, Kerala, India, pp. 259-275.
11.  Aryal, U.K., Shah, S.K., Xu, H.L., and Fujita, M. (2006). Growth, nodulation and mycorrhizal colonization in bean plants improved by rhizobial inoculation with organic and chemical fertilization.  Journal of Sustainable Agriculture, 29(2): 71-83.
12.  Shah, S.K., Shah, R.P., Xu, H.L. and Aryal, U.K. 2006. Biofertilizers: An alternative source of nutrients for sustainable production of tree crops. Journal of Sustainable Agriculture, 29(2): 85-95.
13.  Aryal, U.K. Xu, H.L. and Fujita, M. (2003). Rhizobia and AM fungal inoculation improves growth and nutrient uptake of bean plants under organic fertilization. (2003). Journal of Sustainable Agriculture, 21: 29-41.
14.  Fujiyama, S., Fujita, M. and Aryal, U.K. (2002). Pedosphere in agro-ecosystem. Estimation of food web by measuring 13C and 15N of soil animals and their potential food. (2002). Bulletin of Environmental Sciences 21, 59-64. (In Japanese with English abstract).
15. Aryal, U.K., Hossain, M.K., Mridha, M.A.U., and Xu, H.L. (2000). Nodulation survey and nitrogenase activity of some legume tree species in Bangladesh. Journal of crop Production, 3(1): 325-335.
16.  Aryal, U.K. and Xu, H.L. (2000). Mycorrhizal association and their manipulation for long-term agricultural productivity and sustainability. Journal of Crop Production, 3(1): 285-302.
17.  Aryal, U.K., Hossain, M.K., Mridha, M.A.U., Xu, H.L. and Umemura, H. (1999). Effect of Rhizobium inoculation on growth, nodulation and nitrogenase activity of some legume tree species. Journal of Plant Nutrition, 27 (7): 1049-1059.
18.  Aryal, U.K., Hossain, M.K., Mridha, M.A.U., Xu, H.L. and Umemura, H. (1999). Effect of Rhizoibum inoculation on growth and nodulation of Albizia procera, Albizia lebbeck and Lucaena leucocephala. Pedosphere, 9(2): 153-159.
19.  Hossain, M.K., Hossain, H.S., and Aryal, U.K. (1998). Initial growth performance of eight provenances of Acacia auriculiformis in Chittagong University Campus, Bangladesh. Indian Forester, 124(4): 256-258.