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1.  Evolution of animal Piwi-interacting RNAs and prokaryotic CRISPRs 
Briefings in Functional Genomics  2012;11(4):277-288.
Piwi-interacting RNAs (piRNAs) and CRISPR RNAs (crRNAs) are two recently discovered classes of small noncoding RNA that are found in animals and prokaryotes, respectively. Both of these novel RNA species function as components of adaptive immune systems that protect their hosts from foreign nucleic acids—piRNAs repress transposable elements in animal germlines, whereas crRNAs protect their bacterial hosts from phage and plasmids. The piRNA and CRISPR systems are nonhomologous but rather have independently evolved into logically similar defense mechanisms based on the specificity of targeting via nucleic acid base complementarity. Here we review what is known about the piRNA and CRISPR systems with a focus on comparing their evolutionary properties. In particular, we highlight the importance of several factors on the pattern of piRNA and CRISPR evolution, including the population genetic environment, the role of alternate defense systems and the mechanisms of acquisition of new piRNAs and CRISPRs.
PMCID: PMC3398257  PMID: 22539610
piRNA; CRISPR; co-evolution; transposable elements; phage; plasmids
2.  A Parameter Estimation Technique for Stochastic Self-Assembly Systems and Its Application to Human Papillomavirus Self-Assembly 
Physical biology  2010;7(4):045005.
Virus capsid assembly has been a key model system for studies of complex self-assembly but does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or infer them from the relatively indirect experimental measures available. In the present work, we develop a computational strategy to infer coat-coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient-descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories, and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can infer rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide insight into potential assembly mechanisms of the in vitro system and a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions.
PMCID: PMC3128809  PMID: 21149973
self-assembly; stochastic optimization; human papillomavirus; local rules; parameter fitting
3.  A Comparative Antimicrobial Study on the Essential Oil of the Leaves of Various Species of Cupressus 
Ancient Science of Life  2005;24(3):131-133.
The essential oil of leaves of various cupressus species Viz., C.glauca, C.funebris, C.lawsonia, C. macrocarpa & C. sempervirens have been studied for their antimicrobial activity against certain gram positive [B. substilis, S.aureus], gram negative [E.coli, P.aeruginesa] and fungi (A.niger, A.flavus, C.albicans & A. fumigatus) using two fold serial dilution technique. Our results revealed that, all the species possess significant antibacterial & antifungal activities.
PMCID: PMC3330931  PMID: 22557167
4.  PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes 
Nucleic Acids Research  2004;32(Web Server issue):W318-W320.
An interactive web server is developed for predicting the potential binding sites and its target operons for a given regulatory protein in prokaryotic genomes. The program allows users to submit known or experimentally determined binding sites of a regulatory protein as ungapped multiple sequence alignments. It analyses the upstream regions of all genes in a user-selected prokaryote genome and returns the potential binding sites along with the downstream co-regulated genes (operons). The known binding sites of a regulatory protein can also be used to identify its orthologue binding sites in phylogeneticaly related genomes where the trans-acting regulator protein and cognate cis-acting DNA sequences could be conserved. PredictRegulon can be freely accessed from a link on our world wide web server:
PMCID: PMC441502  PMID: 15215402
5.  Foetal stem cell derivation & characterization for osteogenic lineage 
Background & objectives:
Mesencymal stem cells (MSCs) derived from foetal tissues present a multipotent progenitor cell source for application in tissue engineering and regenerative medicine. The present study was carried out to derive foetal mesenchymal stem cells from ovine source and analyze their differentiation to osteogenic linage to serve as an animal model to predict human applications.
Isolation and culture of sheep foetal bone marrow cells were done and uniform clonally derived MSC population was collected. The cells were characterized using cytochemical, immunophenotyping, biochemical and molecular analyses. The cells with defined characteristics were differentiated into osteogenic lineages and analysis for differentiated cell types was done. The cells were analyzed for cell surface marker expression and the gene expression in undifferentiated and differentiated osteoblast was checked by reverse transcriptase PCR (RT PCR) analysis and confirmed by sequencing using genetic analyzer.
Ovine foetal samples were processed to obtain mononuclear (MNC) cells which on culture showed spindle morphology, a characteristic oval body with the flattened ends. MSC population CD45-/CD14- was cultured by limiting dilution to arrive at uniform spindle morphology cells and colony forming units. The cells were shown to be positive for surface markers such as CD44, CD54, integrinβ1, and intracellular collagen type I/III and fibronectin. The osteogenically induced MSCs were analyzed for alkaline phosphatase (ALP) activity and mineral deposition. The undifferentiated MSCs expressed RAB3B, candidate marker for stemness in MSCs. The osteogenically induced and uninduced MSCs expressed collagen type I and MMP13 gene in osteogenic induced cells.
Interpretation & conclusions:
The protocol for isolation of ovine foetal bone marrow derived MSCs was simple to perform, and the cultural method of obtaining pure spindle morphology cells was established. Criteria proposed for defining MSCs by this study includes the cell adherence to culture plates, specific surface protein profiles and differentiation to osteogenic lineage. The MSCs and osteogenic differentiated cells in this ovine animal model may serve as a large source for stem cell applications in regenerative medical therapies.
PMCID: PMC3657854  PMID: 23563374
Bone marrow; characterization; differentiation; foetal; MACS; mesenchymal stem cells; multilineage; multipotent; osteogenic

Results 1-5 (5)