Project University
Resume:
NEHA JALAN
ab9tf6@r.postjobfree.com
Experience and Projects
*/**** ** *******: Postdoctoral Research Associate, Citrus Research and Education Center, Dept. of
Microbiology and Cell Science, University of Florida, USA
a) Pan genome analysis of multiple isolates of Xanthomonas citri subsp. citri
• DNA extraction and Illumina sequencing of 23 bacterial isolates from around the world causing
citrus canker. I closed, annotated and compared the genomes using various free and professional software
such as CLC Genomics, standalone blast, MAUVE and EDGAR. SNP and DIP analysis and other
comparative analysis such as whole genome phylogeny and pan-genome study was also conducted to
examine geographic evolution and to ascertain differences amongst protein encoding genes particularly
virulence genes.
b) Characterize critical genes involved in release of X. citri subsp. citri from citrus canker lesions.
• Screened a transposon mutant library of over 20,000 mutants for mutants affected in disease
phenotype. Mutants defective in release from canker lesions were selected and DNA extracted to perform
southern blot (confirm single insertion mutation) and characterized the insertion site by rescue cloning.
Complemented the mutants and performed bacterial in planta growth assay, biofilm formation,
extracellular cell wall degrading enzymes, LPS and gum production assays. Host response (citrus) to
mutants analyzed by Microarray, qPCR and microscopy techniques.
c) Whole genome sequencing and characterization of critical genes involved in copper resistance of
Xanthomonas spp. affecting citrus
• I performed de novo sequencing of copper resistant strains causing citrus canker and citrus bacterial
spot using Illumina, 454 pyrosequencing and optical mapping. After finishing and annotating the
sequences the genes in copper resistance operon on the plasmid were further characterized by
bioinformatics comparison and mutational analyses. Whole genome comparison was also done to study
other shared and unique genes in the genome.
8/2008-12/2012: Graduate Research Assistant, Dept. of Microbiology and Cell Science, University of
Florida, USA.
Dissertation: Comparative genomic and transcriptomic analyses of Xanthomonas citri subsp. citri and related
species provide insights into virulence and host-specificity.
a) Whole genome sequencing and comparison of Xanthomonas spp. affecting citrus unique to Florida
• I performed de novo finishing of genomes of isolates unique to Florida using Newbler and CLC
Genomics. Whole genome comparison using MLST phylogenetic analysis, MAUVE, blast, and PCR
amplification to verify and characterize shared and unique genes as compared to highly virulent strains
to find genes that can be used for resistance development. Generated mutants of putative genes to study
their role in pathogenicity. The data was made available to the scientific community through Genbank
and has since been referred by other research publications.
b) RNA-Seq for comparing gene expression of Xanthomonas spp. with different host range and virulence
• Isolated RNA from bacteria grown under different growth conditions, concentrated mRNA and did
Illumina sequencing for RNA-seq. Compared differential gene-expression and statistically analyzed the
data to find relevant genes. Confirmed results by qPCR and biochemical tests.
11/2006-6/2008: Junior Research Fellow, Bhabha Atomic Research Centre and Bhavan’s College,
University of Mumbai, India.
a) Production and radiation effect studies on fructo-oligosaccharide (FOS) polymers and its applications.
• Planning and execution of the project, which included optimization of biopolymer levan production
by Bacillus megaterium type I and develop methods for semi-continuous large-scale production of levan
by immobilization of the culture. Optimized use of radiation technology to produce FOS using levan and
developed a method for purification. Study the effects of radiation on FOS for consumption as a prebiotic
substrate to selectively induce proliferation of probiotic gut flora (Lactobacillus, Bifidobacteria) and
assess its blood biochemistry especially its lipid profile for its hypolipidemic effect by feed trail studies
using albino rat (Wistar strain). Histopathological analysis to check for undue toxicity of radiation
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prepared FOS. Formulation of dough preparation with FOS for its textural and rheological enhancements
to use FOS as gluten (binding agent) during fermentation.
9/2005-10/2006: Lecturer in Microbiology at Sophia College, University of
Mumbai, India.
Lecturer in Industrial Microbiology course for undergraduate students.
Conducted lab classes for all undergraduate microbiology classes with other
lecturers.
Co-conceptualized, secured funding and executed a research project on
“Microbial degradation of Methyl Parathion: Characterization of its metabolites and
their effects on biological system”
Trained and guided 2 masters students for their thesis projects
4/2005-9/2005: Marketing support officer, International Business Pharmaceutics, FDC Ltd., India
Compiled dossiers and resolving queries raised by Health Ministries of multiple
countries.
Assisted and planned promotion of FDC brands in various African countries.
Skills
Laboratory: Molecular cloning and sequencing (sanger), Next-generation sequencing (454, Illumina), Optical
mapping, RNA-seq, comparative genomics, Microarray, Real-time Quantitative PCR (qPCR),
Reverse Transcription PCR (RT-PCR), Southern blot, Multi-locus Sequence Typing (MLST),
DNA primer and probe design, DNA/RNA purification, gel electrophoresis, Light Microscopy,
disease inoculation and analysis (in-planta), culture media design, bacteria pure culture, aseptic
and sterile techniques, bacterial biochemical, enzymatic and characterization assays,
Software: Genomic data analysis with Newbler, CLC Genomics, DNAstar, MAUVE, Mapsolver, EDGAR, R-
package, Clustal, MEGA, NCBI, stand alone blast, phylogenetic analysis, statistical analysis.
Microsoft Office.
Language: English (proficient in oral and written English), Hindi (native speaker)
Education
8/2008-12/2012: Ph.D. in Microbiology and Cell Science, University of Florida, USA.
8/2003 - 5/2005: M.S. in Microbiology, University of Mumbai, India.
8/2000 - 6/2003: B.S. in Microbiology, Mithibai College, University of Mumbai, India
Publications
Research Papers:
1. Jalan N, Blom J, Deng X, Jones JB, Wang N. Comparative genomics of 23 strains of Xanthomonas
citri subsp. citri identifies pan-genome and reveals genomic and evolutionary diversities. (In
preparation).
2. Jalan N, Kumar D, Andrade MO, Yu F, Jones JB, Graham JH, White FF, Setubal JC, Wang N. 2013.
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri
provide insights into mechanisms of bacterial virulence and host range. BMC Genomics. 14:551.
3. Jalan N, Varshney L, Misra N, Paul J, Mitra D, Rairakhwada DD, Bhathena Z,Kumar V. 2013.
Studies on production of fructo-oligosaccharides (FOS) by gamma radiation processing of microbial
levan. Carbohydrate Polymers. 96(1): 365-70.
4. Jalan N, Kumar D, Yu F, Jones JB, Graham JH, Wang N. 2013. Complete genome sequence of
Xanthomonas citri subsp. citri strain AW12879, a restricted-host-range citrus canker causing bacterium.
Genome Announcements. 1(3): e00235-13.
5. Jalan N, Aritua V, Kumar D, Yu F, Jones JB, Graham JH, Setubal JC, Wang N. 2011. Comparative
genomic analysis of Xanthomonas axonopodis pv. citrumelo F1 causing citrus bacterial spot and
related strains provides insights into virulence and host-specificity. Journal of Bacteriology.
193(22): 6342-57.
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Book Chapter:
1. Jalan N, Yan Q, Kogenaru S, Guo Y, Jones JB, Graham JH, Wang N. 2013. Genomics of
Xanthomonas citri and related species. In: Genomes of Plant-Associated Bacteria, D. Gross, A. Lichens-
Park and C. Kole (eds), Springer Publishing Company (in preparation)
Abstracts and Conference Presentations:
1. Jalan N, Deng X, Jones J, Wang N. 2013. Pan-genome analysis of Xanthomonas citri subsp. citri
provides insights into bacterial evolution and pathogenicity. Phytopathology 103:S2.67.
2. Ravindran A, Jalan N, Yuan JS, Wang N, Gross DC. 2013. Complete genome sequencing and
comparative analysis of Pseudomonas syringae pv. syringae strains 301D and HS191. Phytopathology
102:S2.119.
3. Jalan N, Kumar D, Wang N. 2012. Gene content or gene expression, which determines the
difference in host specificity and virulence of strains of Xanthomonas citri subsp. citri? Phytopathology
102:S4.58.
4. Jalan N, Kumar D, Wang N. 2012. Comparative genomic and transcriptomic (RNA-Seq) analyses
reveal the potential host specificity and virulence determinants of Xanthomonas citri subsp. citri.
Graduate Symposium. Dept. of MCS, UF, Florida. 2010.
5. Jalan N, Aritua V, Wang N. 2011. Comparative genomic analysis of Xanthomonas axonopodis pv.
citrumelo strain F1 and other closely related strains. Phytopathology 101:S80.
6. Jalan N, Wang N. 2010. Comparative Genomic Analysis of Xanthomonas axonopodis pv. citri strain
Aw 12879 and Xanthomonas axonopodis pv. citri strain 5208 (Miami). Phytopathology 100:S55.
7. Jalan N, Wang N. Whole genome sequencing and comparative genomic analysis of Xanthomonas
axonopodis pv. citri str. Aw 12879. Graduate Symposium. Dept. of MCS and Dept. of MGM, UF,
Florida. 2010
8. Jalan N, Wang N. Identification and characterization of critical virulence and host specificity genes
of Xanthomonas axonopodis pv. citri and related species. Graduate Student Symposium, Dept. of MCS,
UF, Florida. 2009.
9. Jalan N, Varshney L, Mitra D, Rairakhwada D, Bhathena Z. Studies on Production of Fructo-
oligosaccharides (FOS) by Gamma Radiation Processing of Microbial Levan. Trombay Symposium on
Radiation and Photochemistry (TSRP), India, 2008.
10. Patil R C, Mule A, Gorwalla E, Jalan N, Patil D. Siderophore enhanced wheat juice (Triticum
aestivum) as antimicrobial addendum. National Conference on Medicinal Botnay. India, 2007.
Fellowships and Awards
Student Travel Grant. Graduate Student Council. University of Florida, 2011 and
2012.
Student Travel Award. Dept. of MCS, University of Florida, 2010 and 2012.
Won 2nd place for presentation at Graduate Symposium. Dept. of MCS, University
of Florida, 2010 and 2012.
Junior Research Fellowship, Grant for a two-year project: Fructo-oligosaccharide
production using radiation technology. Board of Research in Nuclear Sciences, DAE,
2006-2008
Mumbai University Teacher fellowship for research project: Microbial
degradation of Methyl Parathion: Characterization of its metabolites and their effects
on biological system. 2006.
Workshops attended/ organized
Attended “Grantsmanship workshop”, 5 May 2011, IFAS, University of Florida,
Gainesville.
Co-moderated an oral technical session on bacteriology/pathogen detection at the
2010 American Phytopathological Society annual meeting.
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Participated in DOE Joint Genome Institute’s Microbial Genomics and
Metagenomics workshop, 1-5th June 2009 at Walnut creek, CA.
Attended the Citrus canker identification and decontamination training course
organized by Institute of Food and Agricultural Sciences. University of Florida. June
2009
Assisted in organizing a National seminar “Biofilms: Challenges and
Applications”, 12-13 January 2007, Department of Microbiology, Bhavan's college,
Mumbai, India. Also, demonstrated the working of Stovall cell assembly, fluorescent
staining and confocal microscopy for study of biofilms.
Supervised a project on Microbial analysis of Kalwa Lake, Thane, for Thane
Municipal Corporation (TMC). India. 2006.
Assisted in organizing a seminar “Biotechnology: The Road Ahead”, 7 January
2006, Dept. of Microbiology, Sophia College, Mumbai, India.
Participated in a six-week summer training course at Bombay Veterinary College,
2004. Trained for techniques like antiserum generation & polyclonal antibody
isolation from chick embryo, viral assays, ELISA, PAGE, serological techniques,
tissue culturing and bacteriological techniques along with animal handling.
Memberships/ Scholarly Societies
2009-present American Phytopathology Society
2010-present American Society for Microbiology
2011-present Toastmasters International
2012- present The Honor Society of Phi Kappa Phi
References available upon request
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