Immunological studies on peroxynitrite modified human DNA

Peroxynitrite (ONOO(-)) is a strong and potent oxidizing and nitrating agent, formed by rapid reaction of two highly reactive, nitric oxide and superoxide anion. The action of peroxynitrite generated by synergistic action of diethylamine NONOate (a nitric oxide donor) and 1,4-hydroquinone (a superoxide donor), on human placental DNA was monitored by ultraviolet and fluorescence spectroscopy, melting temperature studies, S1 nuclease digestibility and alkaline agarose electrophoresis. The peroxynitrite modified human DNA (ONOO(-)-DNA) was found to be highly immunogenic in rabbits inducing high titre immunogen specific antibodies. However, the induced antibodies exhibited appreciable cross-reactivity with various polynucleotides and nucleic acids. The data demonstrate that the antibodies, though cross-reactive, preferentially bind ONOO(-)-modified epitopes on DNA. Visual detection of immune complex formation with native and ONOO(-)-DNA reiterated preferential binding with modified human DNA. DNA modified by ONOO(-) presents unique epitopes which may be one of the factors for the induction of autoantibodies in cancer patients.     

Multiplicity of human immunodeficiency virus infections in lymphoid tissue

Human immunodeficiency virus type 1 (HIV-1)-infected splenocytes in humans were recently shown to harbor three to four proviruses per cell on average (A. Jung et al., Nature 418:144, 2002). However, the mechanisms that lead to such extensive multiple infections are not understood. Here, we find by using mathematical analysis that two mechanisms quantitatively capture the distribution of proviral genomes in HIV-1-infected splenocytes, one where multiple genomes are acquired one at a time in a series of sequential infectious contacts of a target cell with free virions and infected cells, and the other where cell-to-cell transmission of multiple virions or genomes results from a single infectious contact of a target cell with an infected cell. The two mechanisms imply different genetic diversities of proviruses within an infected cell and therefore different rates of emergence of drug resistance via recombination.     

Characterization and in vitro immunomodulatory screening of fructo-oligosaccharides of Asparagus racemosus Willd

Asparagus racemosus Linn. (Fam. Liliaceae) is an ethno-pharmacologically acclaimed Ayurvedic medicinal plant. In the present study, aqueous extract of A. racemosus (ARC) was fractionated and screened for the polysaccharide fraction (ARP). The characterization was done by enzymatic, Size Exclusion, gas chromatography with flame ionization detector (GC-FID), high pressure anion exchange chromatography (HPAEC) and thin layer chromatographic analyses. Phyto-chemical evaluation confirmed the presence of 26.7% of 2 → 1 linked fructo-oligosaccharides (FOS). They have a degree of polymerization (DP) of nearly 7-8. Cytotoxicity evaluation on P388 cell lines was consistent with low cytotoxicity of the extracts. In vitro Natural Killer (NK) cell activity was evaluated using human peripheral blood mononuclear cells (PBMC) isolated from whole blood on a ficoll-hypaque density gradient. K562 a myeloid leukemia cell line, were used as target cells. ARC, tested over the range 0.2-50 μg/ml, showed a dose-related stimulation of NK cell activity with a peak increase of 16.9 ± 4.4% at 5.6 μg/ml. However, ARP demonstrated a higher stimulatory activity of 51.8 ± 1.2% at 25 μg/ml. The results indicate that the FOS from A. racemosus potentiates the NK cell activity and this could be an important mechanism underpinning the ‘Rasayana’ properties of this plant.     

Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities

Fine-mapping studies on four QTLs, qDTY(2.1), qDTY(2.2), qDTY(9.1) and qDTY(12.1), for grain yield (GY) under drought were conducted using four different backcross-derived populations screened in 16 experiments from 2006 to 2010. Composite and bayesian interval mapping analyses resolved the originally identified qDTY(2.1) region of 42.3 cM into a segment of 1.6 cM, the qDTY(2.2) region of 31.0 cM into a segment of 6.7 cM, the qDTY(9.1) region of 32.1 cM into two segments of 9.4 and 2.4 cM and the qDTY(12.1) region of 10.6 cM into two segments of 3.1 and 0.4 cM. Two of the four QTLs (qDTY(9.1) and qDTY(12.1)) having effects under varying degrees of stress severity showed the presence of more than one region within the original QTL. The study found the presence of a donor allele at RM262 within qDTY(2.1) and RM24334 within qDTY(9.1) showing a negative effect on GY under drought, indicating the necessity of precise fine mapping of QTL regions before using them in marker-assisted selection (MAS). However, the presence of sub-QTLs together in close vicinity to each other provides a unique opportunity to breeders to introgress such regions together as a unit into high-yielding drought-susceptible varieties through MAS.     

Cell-type specific roles for PTEN in establishing a functional retinal architecture

Background

The retina has a unique three-dimensional architecture, the precise organization of which allows for complete sampling of the visual field. Along the radial or apicobasal axis, retinal neurons and their dendritic and axonal arbors are segregated into layers, while perpendicular to this axis, in the tangential plane, four of the six neuronal types form patterned cellular arrays, or mosaics. Currently, the molecular cues that control retinal cell positioning are not well-understood, especially those that operate in the tangential plane. Here we investigated the role of the PTEN phosphatase in establishing a functional retinal architecture.

Methodology/Principal Findings

In the developing retina, PTEN was localized preferentially to ganglion, amacrine and horizontal cells, whose somata are distributed in mosaic patterns in the tangential plane. Generation of a retina-specific Pten knock-out resulted in retinal ganglion, amacrine and horizontal cell hypertrophy, and expansion of the inner plexiform layer. The spacing of Pten mutant mosaic populations was also aberrant, as were the arborization and fasciculation patterns of their processes, displaying cell type-specific defects in the radial and tangential dimensions. Irregular oscillatory potentials were also observed in Pten mutant electroretinograms, indicative of asynchronous amacrine cell firing. Furthermore, while Pten mutant RGC axons targeted appropriate brain regions, optokinetic spatial acuity was reduced in Pten mutant animals. Finally, while some features of the Pten mutant retina appeared similar to those reported in Dscam-mutant mice, PTEN expression and activity were normal in the absence of Dscam.

Conclusions/Significance

We conclude that Pten regulates somal positioning and neurite arborization patterns of a subset of retinal cells that form mosaics, likely functioning independently of Dscam, at least during the embryonic period. Our findings thus reveal an unexpected level of cellular specificity for the multi-purpose phosphatase, and identify Pten as an integral component of a novel cell positioning pathway in the retina.     

Deficiency of intramuscular ICC increases fundic muscle excitability but does not impede nitrergic innervation

The motility of the gastrointestinal tract is generated by smooth muscle cells and is controlled to a large extent by an intrinsic neural network. A gap of approximately 200 nm usually separates nerve varicosities from smooth muscle cells, which suggests that direct innervation of the smooth muscle by synapses does not occur. Enteric nerves do make synapse-like contact with proposed regulatory cells, the interstitial cells of Cajal (ICC), which in turn may be in gap junction contact with smooth muscle cells. The role played by ICC in enteric innervation is controversial. Experimental evidence has been presented in vitro for the hypothesis that nitrergic inhibitory innervation is strongly reduced in the absence of ICC. However, in vivo data appear to dispute that. The present report provides evidence that explains the discrepancy between in vivo and in vitro data and provides evidence that inhibitory neurotransmitters can reach smooth muscle cells without hindrance when ICC are absent. The fundic musculature shows increased responses to substance P-mediated innervation and shows marked spontaneous activity, which is consistent with increased muscle excitability.     

Flower bud opening and senescence in roses (Rosa hybrida L.)

The flower is the most significant and beautiful part of plants. Flowers are very useful organs in plant developmental phenomenon. During flower bud opening, various events takes place in a well defined sequence, representing all aspects of plant development, such as cell division, cellular differentiation, cell elongation or expansion and a wide spectrum of gene expression. The complexity of flower bud opening illustrates that various biological mechanisms are involved at different stages. Senescence represents the ultimate stage of floral development and results in wilting or abscission of whole flower or flower parts. Senescence is an active process and governed by a well defined cell death program. Once a flower bud opens, the programmed senescence of petal allows the removal of a metabolically active tissue. In leaves, this process can be reversed, but in floral tissue it cannot, indicating that a highly controlled genetic program for cell death is operating. The termination of a flower involves at least two, sometimes overlapping, mechanisms. In one, the perianth abscises before the majority of its cells initiate a cell death program. Abscission may occur before or during the mobilization of food reserves to other parts of the plant. Alternatively, the petals may be more persistent, so that cell deterioration and food remobilization occur while the petals are still part of the flower. The overall pattern of floral opening varies widely between plant genera, therefore, a number of senescence parameters have been used to group plants into somewhat arbitrary categories. Opening and senescence of rose flower is still an unsolved jigsaw in the world of floriculture industry and the mechanism behind the onset of the very early events in the sequence still remains to be elucidated. Hence, for advancing the knowledge on the pertinent aspect of bud opening and senescence the literature has been cited under this review.     

Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations

An ab initio model for gene prediction in prokaryotic genomes is proposed based on physicochemical characteristics of codons calculated from molecular dynamics (MD) simulations. The model requires a specification of three calculated quantities for each codon: the double-helical trinucleotide base pairing energy, the base pair stacking energy, and an index of the propensity of a codon for protein-nucleic acid interactions. The base pairing and stacking energies for each codon are obtained from recently reported MD simulations on all unique tetranucleotide steps, and the third parameter is assigned based on the conjugate rule previously proposed to account for the wobble hypothesis with respect to degeneracies in the genetic code. The third interaction propensity parameter values correlate well with ab initio MD calculated solvation energies and flexibility of codon sequences as well as codon usage in genes and amino acid composition frequencies in ∼175,000 protein sequences in the Swissprot database. Assignment of these three parameters for each codon enables the calculation of the magnitude and orientation of a cumulative three-dimensional vector for a DNA sequence of any length in each of the six genomic reading frames. Analysis of 372 genomes comprising ∼350,000 genes shows that the orientations of the gene and nongene vectors are well differentiated and make a clear distinction feasible between genic and nongenic sequences at a level equivalent to or better than currently available knowledge-based models trained on the basis of empirical data, presenting a strong support for the possibility of a unique and useful physicochemical characterization of DNA sequences from codons to genomes.