• Naveen Kumar

      Articles written in Journal of Biosciences

    • ARC: Automated Resource Classifier for agglomerative functional classification of prokaryotic proteins using annotation texts

      Muthiah Gnanamani Naveen Kumar Srinivasan Ramachandran

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      Functional classification of proteins is central to comparative genomics. The need for algorithms tuned to enable integrative interpretation of analytical data is felt globally. The availability of a general, automated software with built-in flexibility will significantly aid this activity. We have prepared ARC (Automated Resource Classifier), which is an open source software meeting the user requirements of flexibility. The default classification scheme based on keyword match is agglomerative and directs entries into any of the 7 basic non-overlapping functional classes: Cell wall, Cell membrane and Transporters ($\mathcal{C}$), Cell division ($\mathcal{D}$), Information ($\mathcal{I}$), Translocation ($\mathcal{L}$), Metabolism ($\mathcal{M}$), Stress($\mathcal{R}$), Signal and communication($\mathcal{S}$) and 2 ancillary classes: Others ($\mathcal{O}$) and Hypothetical ($\mathcal{H}$). The keyword library of ARC was built serially by first drawing keywords from Bacillus subtilis and Escherichia coli K12. In subsequent steps, this library was further enriched by collecting terms from archaeal representative Archaeoglobus fulgidus, Gene Ontology, and Gene Symbols. ARC is 94.04% successful on 6,75,663 annotated proteins from 348 prokaryotes. Three examples are provided to illuminate the current perspectives on mycobacterial physiology and costs of proteins in 333 prokaryotes. ARC is available at http://arc.igib.res.in.

    • Nucleic acids in circulation: Are they harmful to the host?

      Indraneel Mittra Naveen Kumar Nair Pradyumna Kumar Mishra

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      It has been estimated that 1011–1012 cells, primarily of haematogenous origin, die in the adult human body daily, and a similar number is regenerated to maintain homeostasis. Despite the presence of an efficient scavenging system for dead cells, considerable amounts of fragmented genetic material enter the circulation in healthy individuals. Elevated blood levels of extracellular nucleic acids have been reported in various disease conditions; such as ageing and age-related degenerative disorders, cancer; acute and chronic inflammatory conditions, severe trauma and autoimmune disorders. In addition to genomic DNA and nucleosomes, mitochondrial DNA is also found in circulation, as are RNA and microRNA. There is extensive literature that suggests that extraneously added nucleic acids have biological actions. They can enter into cells in vitro and in vivo and induce genetic transformation and cellular and chromosomal damage; and experimentally added nucleic acids are capable of activating both innate and adaptive immune systems and inducing a sterile inflammatory response. The possibility as to whether circulating nucleic acids may, likewise, have biological activities has not been explored. In this review we raise the question as to whether circulating nucleic acids may have damaging effects on the host and be implicated in ageing and diverse acute and chronic human pathologies.

    • Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes

      Indraneel Mittra Naveen Kumar Khare Gorantla Venkata Raghuram Rohan Chaubal Fatema Khambatti Deepika Gupta Ashwini Gaikwad Preeti Prasannan Akshita Singh Aishwarya Iyer Ankita Singh Pawan Upadhyay Naveen Kumar Nair Pradyumna Kumar Mishra Amit Dutt

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      Whether nucleic acids that circulate in blood have any patho-physiological functions in the host have not been explored. We report here that far from being inert molecules, circulating nucleic acids have significant biological activities of their own that are deleterious to healthy cells of the body. Fragmented DNA and chromatin (DNAfs and Cfs) isolated from blood of cancer patients and healthy volunteers are readily taken up by a variety of cells in culture to be localized in their nuclei within a few minutes. The intra-nuclear DNAfs and Cfs associate themselves with host cell chromosomes to evoke a cellular DNA-damage-repair-response (DDR) followed by their incorporation into the host cell genomes. Whole genome sequencing detected the presence of tens of thousands of human sequence reads in the recipient mouse cells. Genomic incorporation of DNAfs and Cfs leads to dsDNA breaks and activation of apoptotic pathways in the treated cells. When injected intravenously into Balb/C mice, DNAfs and Cfs undergo genomic integration into cells of their vital organs resulting in activation of DDR and apoptotic proteins in the recipient cells. Cfs have significantly greater activity than DNAfs with respect to all parameters examined, while both DNAfs and Cfs isolated from cancer patients are more active than those from normal volunteers. All the above pathological actions of DNAfs and Cfs described above can be abrogated by concurrent treatment with DNase I and/or anti-histone antibody complexed nanoparticles both in vitro and in vivo. Taken together, our results that circulating DNAfs and Cfs are physiological, continuously arising, endogenous DNA damaging agents with implications to ageing and a multitude of human pathologies including initiation of cancer.

    • Mechanistic role of perfusion culture on bone regeneration


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      Bone tissue engineering (BTE) aims to develop engineered bone tissue to substitute conventional bone grafts. To achievethis, culturing the cells on the biocompatible three-dimensional (3D) scaffold is one alternative approach. The newfunctional bone tissue regeneration could be feasible by the synergetic combinations of cells, biomaterials and bioreactors.Although the field of biomaterial design/development for BTE applications attained reasonable success, development ofsuitable bioreactor remains still a major challenge. Tissue engineering bioreactors provide the microenvironment requiredfor neo-tissue regeneration, and also can be used to study the physio-chemical cues effect on cell proliferation anddifferentiation in order to produce functional tissue. In this direction, various bioreactors have been developed andevaluated for the successful development of engineered bone tissue. Continues assessment of tissue development andlimitations of the bioreactors lead to the progression of perfusion flow bioreactor system. Improvements in perfusion reactorsystem were able to yield multiple tissue engineered constructs with uniform cell distribution, easy to operate protocols andalso effectively handled for the functional tissue development to meet the adequate supply of engineered graft for clinicalapplication.

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