The JAX Synteny Browser for mouse-human comparative genomics

Visualizing regions of conserved synteny between two genomes is supported by numerous software applications. However, none of the current applications allow researchers to select genome features to display or highlight in blocks of synteny based on the annotated biological properties of the features (e.g., type, function, and/or phenotype association). To address this usability gap, we developed an interactive web-based conserved synteny browser, The Jackson Laboratory (JAX) Synteny Browser. The browser allows researchers to highlight or selectively display genome features in the reference and/or the comparison genome according to the biological attributes of the features. Although the current implementation for the browser is limited to the reference genomes for the laboratory mouse and human, the software platform is intentionally genome agnostic. The JAX Synteny Browser software can be deployed for any two genomes where genome coordinates for syntenic blocks are defined and for which biological attributes of the features in one or both genomes are available in widely used standard bioinformatics file formats. The JAX Synteny Browser is available at: http://syntenybrowser.jax.org/. The code base is available from GitHub: https://github.com/TheJacksonLaboratory/syntenybrowser and is distributed under the Creative Commons Attribution license (CC BY).

     

Regulation of the nuclear-coded peptides of yeast cytochrome c oxidase

We have analyzed the catabolite regulation of cytochrome oxidase by assaying changes in the synthesis of precursors of the nuclear-coded peptides (IV--VII) of cytochrome c oxidase in an in vitro reticulocyte cell-free system programmed with RNA isolated from cells grown in either glucose or raffinose. As a first step, we have characterized antibodies which bind to the precursors of subunits V and VI. Initial translation products for subunits IV and VII have also been tentatively identified by utilizing these antibodies. The messenger RNAs coding for the precursors of the nuclear-coded subunits fall in the expected size range of 8--15 S. Catabolite repression of the nuclear-coded oxidase peptides appears to be regulated by the abundance of their messenger RNAs. Translation of messenger RNA isolated from yeast cells grown on glucose indicates a coordinate and uniform increase in precursor synthesis during glucose derepression. In contrast, when RNA isolated from raffinose (derepressed) grown cells is used to direct cell-free translation, precursor abundance is high throughout growth, although the synthesis of some of the species changes in a complex pattern of ratio and abundance. These data indicate that the abundance of the messengers for the nuclear-coded precursors is regulated in a fashion dependent on the physiologic state of the cell.     

Interferon gamma-dependent intestinal pathology contributes to the lethality in bacterial superantigen-induced toxic shock syndrome

Toxic shock syndrome (TSS) caused by the superantigen exotoxins of Staphylococcus aureus and Streptococcus pyogenes is characterized by robust T cell activation, profound elevation in systemic levels of multiple cytokines, including interferon-γ (IFN-γ), followed by multiple organ dysfunction and often death. As IFN-γ possesses pro- as well as anti-inflammatory properties, we delineated its role in the pathogenesis of TSS. Antibody-mediated in vivo neutralization of IFN-γ or targeted disruption of IFN-γ gene conferred significant protection from lethal TSS in HLA-DR3 transgenic mice. Following systemic high dose SEB challenge, whereas the HLA-DR3.IFN-γ(+/+) mice became sick and succumbed to TSS, HLA-DR3.IFN-γ(-/-) mice appeared healthy and were significantly protected from SEB-induced lethality. SEB-induced systemic cytokine storm was significantly blunted in HLA-DR3.IFN-γ(-/-) transgenic mice. Serum concentrations of several cytokines (IL-4, IL-10, IL-12p40 and IL-17) and chemokines (KC, rantes, eotaxin and MCP-1) were significantly lower in HLA-DR3.IFN-γ(-/-) transgenic mice. However, SEB-induced T cell expansion in the spleens was unaffected and expansion of SEB-reactive TCR Vβ8(+) CD4(+) and CD8(+) T cells was even more pronounced in HLA-DR3.IFN-γ(-/-) transgenic mice when compared to HLA-DR3.IFN-γ(+/+) mice. A systematic histopathological examination of several vital organs revealed that both HLA-DR3.IFN-γ(+/+) and HLA-DR3.IFN-γ(-/-) transgenic mice displayed comparable severe inflammatory changes in lungs, and liver during TSS. Remarkably, whereas the small intestines from HLA-DR3.IFN-γ(+/+) transgenic mice displayed significant pathological changes during TSS, the architecture of small intestines in HLA-DR3.IFN-γ(-/-) transgenic mice was preserved. In concordance with these histopathological changes, the gut permeability to macromolecules was dramatically increased in HLA-DR3.IFN-γ(+/+) but not HLA-DR3.IFN-γ(-/-) mice during TSS. Overall, IFN-γ seemed to play a lethal role in the immunopathogenesis of TSS by inflicting fatal small bowel pathology. Our study thus identifies the important role for IFN-γ in TSS.     

Gossypol mediated DNA degradation

Gossypol, a polyphenolic compound isolated from cotton plant was found to degrade pBR322 DNA in vitro in a reaction which required the presence of a metal ion, a reducing agent (2-mercaptoethanol) and oxygen as revealed after agarose gel electrophoresis. Fe3+ and Co2+ showed maximum degradation whereas addition of Ca2+ and Mg2+ prevented the gossypol mediated DNA damage. Gossypol caused degradation of rat liver DNA incubated in vitro even in the absence of added metal ions and 2-mercaptoethanol. Incubation of intact rat liver nuclei with gossypol revealed DNA degradation and nuclei isolated from rats treated with gossypol in vivo showed higher susceptibility to DNA fragmentation when incubated with gossypol in vitro than control nuclei. EcoR1 and AIuI digestion of DNA isolated from gossypol treated rats gave clear cut evidence for DNA degradation. These observations indicate that gossypol is genotoxic and considerable care has to be exercised in its use.     

Green synthesis,characterization and biological activity of Solanum trilobatum-mediated silver nanoparticles

Biologically inspired synthesis of nanoparticles was found to be more attractive in metal nanoparticle synthesis. The present study reported an in-situ biogenic synthesis of silver nanoparticles (AgNPs) using Solanum trilobatum aqueous leaf extract. On this basis, the aqueous leaf extract of S. trilobatum acted as a reducing agent and stabilizing agent to synthesize highly stable AgNPs at ambient temperature. Eventually, the synthesized and stabilized AgNPs surface plasmon resonance was near 430 nm through a UV–visible (UV–vis) spectrophotometer. Here, the stability of the silver colloids monitored through zeta potential and mean particle size was evaluated through diffraction light scattering (DLF). Further, the average particle size was found to be 27.6 nm and spherical, confirmed with transmission electron microscopy (TEM). Also, colloidal AgNPs and aqueous extract are found to be rich sources of antioxidants and exhibit higher free radical scavenging ability. Thus, efficient inhibition with COX1 and COX2 enzymes and the protective effect with human red blood cell (HRBC) membrane stability showed significant results. These features are promising, suggesting the possibility of the AgNPs to be useful to disease-modifying for treating inflammatory disorders and associated complications.     

2′-Fluoro-6′-methylene-carbocyclic adenosine phosphoramidate (FMCAP) prodrug: In vitro anti-HBV activity against the lamivudine–entecavir resistant triple mutant and its mechanism of action

Novel 2′-fluoro-6′-methylene-carbocyclic adenosine (FMCA) monophosphate prodrug (FMCAP) was synthesized and evaluated for its in vitro anti-HBV potency against a lamivudine–entecavir resistant clone (L180M + M204V + S202G). FMCA demonstrated significant antiviral activity against wild-type as well as lamivudine–entecavir resistant triple mutant (L180M + M204V + S202G). The monophosphate prodrug (FMCAP) demonstrated greater than 12-fold (12×) increase in anti-HBV activity without increased cellular toxicity. Mitochondrial and cellular toxicity studies of FMCA indicated that there is no significant toxicity up to 100 μM. Mode of action studies by molecular modeling indicate that the 2′-fluoro moiety by hydrogen bond as well as the Van der Waals interaction of the carbocyclic ring with the phenylalanine moiety of the polymerase promote the positive binding, even in the drug-resistant mutants.     

Exit fluence analysis using portal dosimetry in volumetric modulated arc therapy

AimIn measuring exit fluences, there are several sources of deviations which include the changes in the entrance fluence, changes in the detector response and patient orientation or geometry. The purpose of this work is to quantify these sources of errors.BackgroundThe use of the volumetric modulated arc therapy treatment with the help of image guidance in radiotherapy results in high accuracy of delivering complex dose distributions while sparing critical organs. The transit dosimetry has the potential of Verifying dose delivery by the linac, Multileaf collimator positional accuracy and the calculation of dose to a patient or phantom.Materials and methodsThe quantification of errors caused by a machine delivery is done by comparing static and arc picket fence test for 30 days. A RapidArc plan, created for the pelvis site was delivered without and with Rando phantom and exit portal images were acquired. The day to day dose variation were analysed by comparing the daily exit dose images during the course of treatment. The gamma criterion used for analysis is 3% dose difference and 3 mm distance to agreement with a threshold of 10% of maximum dose.ResultsThe maximum standard deviation for the static and arc picket fence test fields were 0.19 CU and 1.3 CU, respectively. The delivery of the RapidArc plans without a phantom shows the maximum standard deviation of 1.85 CU and the maximum gamma value of 0.59. The maximum gamma value for the RapidArc plan delivered with the phantom was found to be 1.2. The largest observed fluence deviation during the delivery to patient was 5.7% and the maximum standard deviation was 4.1 CU.ConclusionIt is found from this study that the variation due to patient anatomy and interfraction organ motion is significant.