Palli, Subba R

Projects in the laboratory of Dr. S.R. Palli, Department of Entomology

1. Molecular Modeling of Insect proteins and virtual Screening for the identification of potential inhibitors of Aedes aegypti Receptors.

The study involves structure based modeling of insect proteins using Molecular Dynamics Simulations. For the preliminary investigations, 20 ligands for three different proteins would be optimized using Gaussian software. Protein-Ligand complexes of optimized inhibitors would be simulated using AMBER12. The docked confirmations would be further studied using MMPBSA methodology. Modules for Gauss and AMBER12 are available on DLX clusters. High-throughput screening (HTS) of large chemical libraries from ZINC database would be investigated to identify Insect Molecular targets. The study requires very robust and high accuracy docking tools for the identification of novel drug candidates. We plan to use Surflex-dock, an automated tool for HTS screening to identify top 100 potential inhibitors, which would be further, studied using Molecular Dynamics Simulations in AMBER12. However, Surflex-Dock is not available on DLX cluster and addition of this software to the DLX cluster could be of great importance to many groups attempting screening of large chemical databases.

Research Personnel:

Amit Roy, postdoc
Melise Lecheta, Postdoc
Micheal Sheetz (Research Scientis III)
Vikram Gazula (IT Manager III)

2. Colorado potato beetle (CPB) Genome Project

CPB genome project is a part of I5K project. We received the CPB RNAseq data from the I5K project. Our role towards this research project is to provide the transcriptome assembly and automated annotation. This information will be available later on our University website to benefit other researchers. In order to achieve our goal we have used the following software that were downloaded on the supercomputer:

Students:

Megha Kalsi (Graduate student)

Jiao Yaoyu (Graduate Student 01/07/19) - 81080-rpalli-uksr
Shankar Chaitan R Chereddy

Masti Venugopal Srihari Sharma, Added on the MCC cluster 04/17/2023

Callista W Vandegriff, Graduate, Added on MCC cluster 08/01/2023

Software:

Velvet assembler: for short read sequence assembly
Oasis: for short read sequence assembly
NCBI blast: gene annotation i.e. finding region of sequence similarity and yielding structural and functional information about the novel sequence

These programs were freely downloadable from the respective websites. No publications yet on the data generated using these programs on DLX.

3. Analysis of Bed bug genome and transcriptome data.

Work on DLX cluster involves :
Work mainly involves identification of genes from transcriptome and genome of bed bug mainly by using BLAST. Expression analyses of transcriptome data from different traeatment groups. Current project involves identification of miRNAs.

Research Personnel:

Amit Roy, postdoc

Masti Venugopal Srihari Sharma, added on MCC cluster, 04/17/2023

Software:

1. Transcriptome analyses of illumina data using velvet, oasis, ncbi blast and RSEM.
2. Genome analysis using ncbi blast and mirdeep.

Publication:

2014

1. Palli, S.R. (2014) RNA interference in Colorado potato beetle: steps towards development of dsRNA as a commercial insecticide. Current Opinions in Insect Science (In press).
2. Li Z, Ge X, Ling L, Zeng B, Xu J, Aslam AF, You L, Palli SR, Huang Y, Tan A. (2014) CYP18A1 regulates tissue-specific steroid hormone inactivation in Bombyx mori. Insect Biochem Mol Biol. 2014 Aug 27;54C:33-41. doi: 10.1016/j.ibmb.2014.08.007. Epub ahead of print
3. 3.He Q, Wen D, Jia Q, Cui C, Wang J, Palli SR, Li S. (2014) Heat Shock Protein 83 (Hsp83) Facilitates Methoprene-tolerant (Met) Nuclear Import to Modulate Juvenile Hormone Signaling. J Biol Chem. 2014 Aug 13. pii: jbc.M114.582825. Epub ahead of print.
4. Cui, Y., Sui, Y., Xu, J., Zhu, F., Palli, S.R. (2014). Juvenile hormone regulates Aedes aegypti Kruppel homolog 1 through a conserved E box motif. Insect Biochem Mol Biol 52C, 23-32.
5. Shukla, J.N., Palli, S.R. (2014) Production of all female progeny: an evidence for the presence of male sex determination factor on Y chromosome. J. Exp. Biol.217, 1653-1655.

2013

6. Shukla, J.N., Palli, S.R. (2013) Tribolium castaneum transformer-2 regulates sex determination and development in both males and females. Insect Biochem. Mol. Biol. 42, 1125-1132.
7. Xu J, Sheng Z, Palli S.R. (2013) Juvenile hormone and insulin regulate trehalose homeostasis in the red flour beetle, Tribolium castaneum. PLoS Genet. 9, e1003535.
8. Parthasarathy R., Farkas, R. and Palli, S.R. (2013) Recent Progress in Juvenile hormone analogs (JHA) research. Adv. Insect Physiol. 43, 353-436.
9. Zhu F, Moural TW, Shah K, Palli SR (2013) Integrated analysis of cytochrome P450 gene superfamily in the red flour beetle, Tribolium castaneum. BMC Genomics. 14:174-182.
10. Zhu F, Gujar H, Gordon JR, Haynes KF, Potter MF, Palli SR (2013) Bed bugs evolved unique adaptive strategy to resist pyrethroid insecticides. Sci Rep. 3:1456.
11. Jindra, M., Palli, S.R., and Riddiford, L.M. (2013). The Juvenile Hormone Signaling Pathway in Insect Development. Ann. Rev. Entomol 58:181-204.
12. Xu, J., Baulding, J. & Palli, S. R. (2013) Proteomics of Tribolium castaneum seminal fluid proteins: Identification of an angiotensin-converting enzyme as a key player in regulation of reproduction, Journal of proteomics. 78C, 83-93.

2012

1. Zhu et al 2012; Bed bugs evolved unique adaptive strategy to resist pyrethroid insecticides
http://www.nature.com/srep/2013/130314/srep01456/full/srep01456.html

Grants

Palli, Subba R 400-41-08-41-6673 Mechanisms of RNA interference Iowa State University 1/1/2014 - 12/31/2015 $120,000
Palli, Subba R 58-1245-4-102 Development of Novel Insecticide Synergistic for Resistance Management Agricultural Research Service 9/1/2014 - 8/30/2015 $130,000
Palli, Subba R IIP-1338766 REU: Center for Arthropod Management Technologies National Science Foundation 8/22/2013 - 7/31/2018 SCOPE
Palli, Subba R SUBAWARD #6408-1070-00-A Ecdysteroid signaling in Filarial parasites University of South Florida 8/15/2013 - 7/31/2015 $16,263
Palli, Subba R IIP-1338766 Center for Arthropod Management Technologies National Science Foundation 8/1/2013 - 7/31/2018 $308,000
Palli, Subba R 58-1245-3-011 P450 inhibition assays Agricultural Research Service 2/1/2013 - 9/30/2014 $125,918
Palli, Subba R IOS-0421856 20 Hydroxyecdysone Suppression of Juvenile Hormone Response $928,294 National Science Foundation 8/1/2004 - 7/31/2014
Palli, Subba R 5 R01 GM070559-09 Molecular Analysis of Juvenile Hormone Action $852,776 National Institute of General Medical Sciences 2/1/2010 1/31/2015
Palli, Subba R 2011-67013-30143 Molecular Analysis of Xenobiotic Response in the Colorado Potato Beetle $456,364 National Institute of Food and Agriculture 2/15/2011 2/14/2015
Palli, Subba R 58-1245-3-011 P450 inhibition assays $80,918 Agricultural Research Service 2/1/2013 8/30/2014