Histone Acetyl Transferase 1 Is Essential for Mammalian Development,Genome Stability,and the Processing of Newly Synthesized Histones H3 and H4

Histone acetyltransferase 1 is an evolutionarily conserved type B histone acetyltransferase that is thought to be responsible for the diacetylation of newly synthesized histone H4 on lysines 5 and 12 during chromatin assembly. To understand the function of this enzyme in a complex organism, we have constructed a conditional mouse knockout model of Hat1. Murine Hat1 is essential for viability, as homozygous deletion of Hat1 results in neonatal lethality. The lungs of embryos and pups genetically deficient in Hat1 were much less mature upon histological evaluation. The neonatal lethality is due to severe defects in lung development that result in less aeration and respiratory distress. Many of the Hat1^−/− neonates also display significant craniofacial defects with abnormalities in the bones of the skull and jaw. Hat1^−/− mouse embryonic fibroblasts (MEFs) are defective in cell proliferation and are sensitive to DNA damaging agents. In addition, the Hat1^−/− MEFs display a marked increase in genome instability. Analysis of histone dynamics at sites of replication-coupled chromatin assembly demonstrates that Hat1 is not only responsible for the acetylation of newly synthesized histone H4 but is also required to maintain the acetylation of histone H3 on lysines 9, 18, and 27 during replication-coupled chromatin assembly.     

GiRaF: robust, computational identification of influenza reassortments via graph mining

Reassortments in the influenza virus--a process where strains exchange genetic segments--have been implicated in two out of three pandemics of the 20th century as well as the 2009 H1N1 outbreak. While advances in sequencing have led to an explosion in the number of whole-genome sequences that are available, an understanding of the rate and distribution of reassortments and their role in viral evolution is still lacking. An important factor in this is the paucity of automated tools for confident identification of reassortments from sequence data due to the challenges of analyzing large, uncertain viral phylogenies. We describe here a novel computational method, called GiRaF (Graph-incompatibility-based Reassortment Finder), that robustly identifies reassortments in a fully automated fashion while accounting for uncertainties in the inferred phylogenies. The algorithms behind GiRaF search large collections of Markov chain Monte Carlo (MCMC)-sampled trees for groups of incompatible splits using a fast biclique enumeration algorithm coupled with several statistical tests to identify sets of taxa with differential phylogenetic placement. GiRaF correctly finds known reassortments in human, avian, and swine influenza populations, including the evolutionary events that led to the recent 'swine flu' outbreak. GiRaF also identifies several previously unreported reassortments via whole-genome studies to catalog events in H5N1 and swine influenza isolates.     

Electrophoretic fabrication of chitosan-zirconium-oxide nanobiocomposite platform for nucleic acid detection

The present work describes electrophoretic fabrication of nanostructured chitosan-zirconium-oxide composite (CHIT-NanoZrO(2)) film (180 nm) onto indium-tin-oxide (ITO)-coated glass plate. This nanobiocomposite film has been explored as immobilization platform for probe DNA specific to M. Tuberculosis as model biomolecule to investigate its sensing characteristics. It is revealed that pH-responsive behavior of CHIT and its cationic skeleton is responsible for the movement of CHIT-NanoZrO(2) colloids toward cathode during electrophoretic deposition. The FT-IR, SEM, TEM, and EDX techniques have been employed for the structural, morphological, and composition analysis of the fabricated electrodes. The morphological studies clearly reveal uniform inter-linking and dispersion of hexagonal nanograins of ZrO(2) (30-50 nm) into the chitosan matrix, resulting in homogeneous nanobiocomposite formation. Electrochemical response measurements of DNA/CHIT-NanoZrO(2)/ITO bioelectrode, carried out using cyclic voltammetry and differential pulse voltammetry, reveal that this bioelectrode can specifically detect complementary target DNA up to 0.00078 μM with sensitivity of 6.38 × 10(-6) AμM(-1).     

Comparison of virokine from camel pseudocowpoxvirus (PCPV) with Interleukin 10 of the Dromedary camel (Camelus dromedarius)

Cellular interleukin-10 (IL-10) gene from the peripheral blood mononuclear cells of the healthy Dromedary camel (Camelus dromedarius) and viral IL-10 (vIL-10) from the skin scabs of the Dromedary camels infected with contagious ecthyma (a parapoxviral infection in the camels) were amplified by polymerase chain reaction, cloned and characterized. Sequence analysis revealed that the open reading frame (ORF) of dromedarian camel IL-10 is 537 bp in length, encoding 178 amino acid polypeptide while open reading frame of vIL-10 from camel is 561 bp, encoding 187 amino acid polypeptide. The Dromedary camel IL-10 exhibited 62.6% and 68.5% sequence identity at the nucleotide and amino acid level, respectively, with vIL-10 from camel. Sequence analysis also revealed that the Dromedary camel IL-10 shared 99.4% and 98.3% identity at the nucleotide and amino acid level, respectively, with the Bactrian camel (Camelus bactrianus). But vIL-10 from camel shared 84.7% and 83.4% sequence identity at the nucleotide and amino acid level, respectively, with vIL-10 from reindeer (Rangifer tarandus), which is a ruminant species belonging to the order Artiodactyla. The present study was conducted to evaluate the evolutionary origin of the camel parapoxvirus with parapoxviruses of cattle and sheep and the resultant sequence analysis revealed that camel parapoxvirus is closely related to cattle parapoxvirus than sheep parapoxvirus (Orf virus).     

Bioinformatics and molecular biology for the quantification of closely related bacteria

Molecular biological methods for mixed culture analysis outshine conventional culture-based techniques in terms of better sensitivity and reliability. The majority of these methods exploit the 16S rRNA sequences of the community DNA, which often fall short for the analysis of closely related microorganisms. This research details the development and validation of a comprehensive methodology to differentiate and quantitatively characterize two Pseudomonas species in a mixed culture. A bioinformatics tool based on whole-genome polymorphism comparison was used to identify marker sequences to differentiate the two bacteria using quantitative real-time PCR. The quantification of the two species was achieved through a correlation of the genomic DNA versus cell number (genomic DNA purification) and threshold cycle number versus genomic DNA (real-time PCR). Several factors including the limitation of genomic DNA purification, effects of substrate concentrations and growth phase on cellular DNA, and choice of simplex or duplex reaction for real-time PCR were considered and evaluated. The developed method was experimentally validated against synthetically constructed consortia.     

Computational and in vitro insights on snake venom phospholipase A2 inhibitor of phytocompound ikshusterol3-O-glucoside of Clematis gouriana Roxb. ex DC.

Ikshusterol3-O-glucoside was isolated from Clematis gouriana Roxb. ex DC. root. A structure of the isolated compound was determined on the basis of various spectroscopic interpretations (UV, NMR, FTIR, and GC-MS-EI). This structure was submitted in the PubChem compound database (SID 249494133). SID 249494133 was carried out by density functional theory calculation to observe the chemical stability and electrostatic potential of this compound. The absorption, distribution, metabolism, and excretion property of this compound was predicted to evaluate the drug likeness and toxicity. In addition, molecular docking, quantum polarized ligand docking, prime MMGBSA calculation, and induced fit docking were performed to predict the binding status of SID 249494133 with the active site of phospholipase A₂ (PLA₂) (PDB ID: 1A3D). The stability of the compound in the active site of PLA₂ was carried out using molecular dynamics simulation. Further, the anti-venom activity of the compound was assessed using the PLA₂ assay against Naja naja (Indian cobra) crude venom. The results strongly show that Ikshusterol3-O-glucoside has a potent snake-venom neutralizing capacity and it might be a potential molecule for the therapeutic treatment for snakebites.