ANNUAL REPORT - Department of Biotechnology

profiling of the outer membrane proteins of
Acinetobacter baumannii in native strain and its βlactam
resistant strains using SDS PAGE has been
carried out by a group at AIIMS, New Delhi. The
resistant groups were characterized according to
their outer membrane profiles and designation of
profiles as A (ATCC type), A2 (ATCC type with
prevalence of high molecular weight proteins) and U
(Unusual profiling). Proteins of native and resistant
strains have been identified and structural and
functional characterization of OmpAb protein of
native strain has been carried out.
A combined approach of genomics and proteomics
was used to understand the role of geneenvironment
interactions in Parkinson's disease
(PD). Several genes and proteins were identified that
participate in pesticide induced PD. The study
highlighted the contribution of several genes and
proteins in understanding the basic mechanism of
PD. Proteome profiles of striatal tissues were
compared and differentially expressed proteins were
identified. Three proteins significantly down
regulated in treated groups were identified as -
enolase, glia maturation factor β (GMF-β) and
complexin-I. The differential expressions of these
proteins were also validated. Microarray profiling
was done in the striatal tissues of animals treated
with maneb+paraquat for 3, 6 and 9 weeks and upregulation/down-regulation
of several genes
including those involved in neuronal/apoptotic
pathways were identified. Some sets of treated
animals were further treated with L-DOPA and a
significant alteration in protein and gene expression
profiles were observed.
Oral cancer is a major global health problem with no
marked improvement in five year survival rates over
the past decade. Understanding the molecular
mechanisms involved in invasion and loco regional
spread of oral tumors will pave the way for
identification of key proteins implicated in these
processes. A research group at AIIMS has recently
identified some novel proteins in oral carcinomas
that may be involved in interacellular adhesion and
communication using high throughput gene
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expression profiling. This study is designed to test
the hypothesis that these differentially expressed
proteins (14-3-3 zeta and ALCAM) play an important
role in the development and progression of oral
cancer, either directly or by interacting with other
cellular proteins, involved in cytoskeletal
reorganization and loco regional spread of oral
carcinomas.
In “The Mycobacterium w genome program:
complete genome sequencing and comparative
genomics”, 10X sequence has been completed with
a sequencing efficiency of 87.84% and total
sequence coverage of over 6 Mb. An extensive study
of scaffolds and their linking pattern with 562 contigs
from 10X assembly has been carried out which
shows that the assembly has almost reached a
plateau in terms of its lateral expansion in size and
the total genome size of around 6 Mb has been
expected. There are a total of 82 contigs oriented in
the 24 scaffolds covering around 5.75 Mb (95.5%) of
the genome sequenced with the largest scaffold of
about 1.3 Mb in size. There are 58 sequencing gaps
and 24 physical gaps in the genome data at the 10X
stage of assembly that need to be filled to obtain a
finished quality sequence and to carry out annotation
work. The preliminary analysis of the sequencing
gaps show that 22 out of these 58 have linking sub
clones of a 5 kb library and the remaining 36 are
linked by 2 kb sub clones. The detailed analysis and
targeted gap filling for the same is currently under
process. So far, information about sequencing gaps
(58) and physical gaps (14) have been generated.
Phylogenetic analyses based on high-resolution
genome fingerprinting by FAFLP analysis, ERIC
typing, and sequence analyses with the help of
candidate gene sequencing like 16S rRNA, hsp65
and rpoB point to its relatedness to the M. avium
complex. The study of genome assemblage trend of
Mw indicates a size ~6.0 Mb which points to the
possibility of Mw being the predecessor of M. avium
complex species. This is an interesting observation
considering the opportunistic nature of members of
M. avium complex in contrast to a non-pathogenic
attribute of Mw.
Research and Development