'DNA' as contaminants in antibiotics and its capacity to transform bacteria to drug resistance

DNA/and deoxyribose sugars were detected in streptomycin (Sm), kanamycin, polymyxin, penicillin G, ampicillin, methicillin, cloxacillin and mitomycin C in small amounts/traces. Stained DNA could be feebly visualized directly in Sm run in agarose gel, which improved after its separation and concentration. These DNA materials were DNase sensitive, RNase and pronase resistant, and appeared to consist of fragments, c. less than or equal to 6 Mdal; this could repeatedly transform to SmR several recipient enterobacteria and vibrios; E. coli C600 and S. typhi 57, after such transformation revealed similar plasmid DNA bands that were absent in their wild-types. G + C mole% of plasmid and chromosomal DNA of recipient (57) along with that of Streptomyces griseus reference strain, suggested an extraneous origin for the plasmid DNA.     

A Simple Alternative to Stereotactic Injection for Brain Specific Knockdown of miRNA

MicroRNAs (miRNAs) are key regulators of gene expression. In the brain, vital processes like neurodevelopment and neuronal functions depend on the correct expression of microRNAs. Perturbation of microRNAs in the brain can be used to model neurodegenerative diseases by modulating neuronal cell death. Currently, stereotactic injection is used to deliver miRNA knockdown agents to specific location in the brain. Here, we discuss strategies to design antagomirs against miRNA with locked nucleotide modifications (LNA). Subsequently describe a method for brain specific delivery of antagomirs, uniformly across different regions of the brain. This method is simple and widely applicable since it overcomes the surgery, associated injury and limitation of local delivery in stereotactic injections. We prepared a complex of neurotropic, cell-penetrating peptide Rabies Virus Glycoprotein (RVG) with antagomir against miRNA-29 and injected through tail vein, to specifically deliver in the brain. The antagomir design incorporated features that allow specific targeting of the miRNA and formation of non-covalent complexes with the peptide. The knock-down of the miRNA in neuronal cells, resulted in apoptotic cell death and associated behavioural defects. Thus, the method can be used for acute models of neuro-degeneration through the perturbation of miRNAs.     

Antagomirbase- a putative antagomir database

The accurate prediction of a comprehensive set of messenger putative antagomirs against microRNAs (miRNAs) remains an open problem. In particular, a set of putative antagomirs against human miRNA is predicted in this current version of database. We have developed Antagomir database, based on putative antagomirs-miRNA heterodimers. In this work, the human miRNA dataset was used as template to design putative antagomirs, using GC content and secondary structures as parameters. The algorithm used predicted the free energy of unbound antagomirs. Although in its infancy the development of antagomirs, that can target cell specific genes or families of genes, may pave the way forward for the generation of a new class of therapeutics, to treat complex inflammatory diseases. Future versions need to incorporate further sequences from other mammalian homologues for designing of antagomirs for aid in research. AVAILABILITY: The database is available for free at http://bioinfopresidencycollegekolkata.edu.in/antagomirs.html.     

Genetic diversity and selection at the Plasmodium vivax apical membrane antigen-1 (PvAMA-1) locus in a Sri Lankan population

Plasmodium vivax apical membrane antigen 1 (PvAMA-1) is an important malaria vaccine candidate. We present the first comprehensive analysis of nucleotide diversity across the entire PvAMA-1 gene using a single population sample from Sri Lanka. In contrast to what has been observed at the AMA-1 locus of Plasmodium falciparum, the signature of diversifying selection is seen most strongly in Domain II of PvAMA-1, indicating that the different domains in each species may be subject to varying selective pressures and functional constraints. We also find that recombination plays an important role in generating haplotype diversity at this locus, even in a region of low endemicity such as Sri Lanka. Mapping of diversity and recombination hotspots onto a 3-dimensional structural model of the protein indicates that one surface of the molecule may be particularly likely to bear epitopes for antibody recognition. Regions of this surface that show constrained variability may prove to be promising vaccine targets.     

Properties of Bacillus anthracis spores prepared under various environmental conditions

Bacillus anthracis makes highly stable, heat-resistant spores which remain viable for decades. Effect of various stress conditions on sporulation in B. anthracis was studied in nutrient-deprived and sporulation medium adjusted to various pH and temperatures. The results revealed that sporulation efficiency was dependent on conditions prevailing during sporulation. Sporulation occurred earlier in culture sporulating at alkaline pH or in PBS than control. Spores formed in PBS were highly sensitive towards spore denaturants whereas, those formed at 45°C were highly resistant. The decimal reduction time (D-10 time) of the spores formed at 45°C by wet heat, 2 M HCl, 2 M NaOH and 2 M H₂O₂ was higher than the respective D-10 time for the spores formed in PBS. The dipicolinic acid (DPA) content and germination efficiency was highest in spores formed at 45°C. Since DPA is related to spore sensitivity towards heat and chemicals, the increased DPA content of spores prepared at 45°C may be responsible for increased resistance to wet heat and other denaturants. The size of spores formed at 45°C was smallest amongst all. The study reveals that temperature, pH and nutrient availability during sporulation affect properties of B. anthracis spores.