Targeting the Ets Binding Site of the HER2/neu Promoter with Pyrrole-Imidazole Polyamides

Three DNA binding polyamides (1-3) were synthesized that bind with high affinity (Ka = 8.7·10^9 M^-1 to 1.4·10^10 M^-1) to two 7-base pair sequences overlapping the Ets DNA binding site (EBS; GAGGAA) within the regulatory region of the HER2/neu proximal promoter. As measured by electrophoretic mobility shift assay, polyamides binding to flanking elements upstream (1) or downstream (2 and 3) of the EBS were one to two orders of magnitude more effective than the natural product distamycin at inhibiting formation of complexes between the purified EBS protein, epithelial restricted with serine box (ESX), and the HER2/neu promoter probe. One polyamide, 2, completely blocked Ets-DNA complex formation at 10 nM ligand concentration, whereas formation of activator protein-2-DNA complexes was unaffected at the activator protein-2 binding site immediately upstream of the HER2/neu EBS, even at 100 nM ligand concentration. At equilibrium, polyamide 1 was equally effective at inhibiting Ets/DNA binding when added before or after in vitro formation of protein-promoter complexes, demonstrating its utility to disrupt endogenous Ets-mediated HER2/neu preinitiation complexes. Polyamide 2, the most potent inhibitor of Ets-DNA complex formation by electrophoretic mobility shift assay, was also the most effective inhibitor of HER2/neu promoter-driven transcription measured in a cell-free system using nuclear extract from an ESX- and HER2/neu-overexpressing human breast cancer cell line, SKBR-3

Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes

BACKGROUND: Pectin-rich agricultural wastes potentially represent favorable feedstocks for the sustainable production of alternative energy and bio-products. Their efficient utilization requires the conversion of all major constituent sugars. The current inability of the popular fermentation host Saccharomyces cerevisiae to metabolize the major pectic monosaccharide D-galacturonic acid (D-GalA) significantly hampers these efforts. While it has been reasoned that the optimization of cellular D-GalA uptake will be critical for the engineering of D-GalA utilization in yeast, no dedicated eukaryotic transport protein has been biochemically described. Here we report for the first time such a eukaryotic D-GalA transporter and characterize its functionality in S. cerevisiae. RESULTS: We identified and characterized the D-GalA transporter GAT-1 out of a group of candidate genes obtained from co-expression analysis in N. crassa. The N. crassa Δgat-1 deletion strain is substantially affected in growth on pectic substrates, unable to take up D-GalA, and impaired in D-GalA-mediated signaling events. Moreover, expression of a gat-1 construct in yeast conferred the ability for strong high-affinity D-GalA accumulation rates, providing evidence for GAT-1 being a bona fide D-GalA transport protein. By recombinantly co-expressing D-galacturonate reductase or uronate dehydrogenase in yeast we furthermore demonstrated a transporter-dependent conversion of D-GalA towards more reduced (L-galactonate) or oxidized (meso-galactaric acid) downstream products, respectively, over a broad concentration range. CONCLUSIONS: By utilizing the novel D-GalA transporter GAT-1 in S. cerevisiae we successfully generated a transporter-dependent uptake and catalysis system for D-GalA into two products with high potential for utilization as platform chemicals. Our data thereby provide a considerable first step towards a more complete utilization of biomass for biofuel and value-added chemicals production

What Can the Accretion Induced Collapse of White Dwarfs Really Explain?

The accretion induced collapse (AIC) of a white dwarf into a neutron star has been invoked to explain gamma-ray bursts, Type Ia supernovae, and a number of problematic neutron star populations and specific binary systems. The ejecta from this collapse has also been claimed as a source of r-process nucleosynthesis. So far, most AIC studies have focussed on determining the event rates from binary evolution models and less attention has been directed toward understanding the collapse itself. However, the collapse of a white dwarf into a neutron star is followed by the ejection of rare neutron-rich isotopes. The observed abundance of these chemical elements may set a more reliable limit on the rate at which AICs have taken place over the history of the galaxy. In this paper, we present a thorough study of the collapse of a massive white dwarf in 1- and 2-dimensions and determine the amount and composition of the ejected material. We discuss the importance of the input physics (equation of state, neutrino transport, rotation) in determining these quantities. These simulations affirm that AICs are too baryon rich to produce gamm-ray bursts and do not eject enough nickel to explain Type Ia supernovae (with the possible exception of a small subclass of extremely low-luminosity Type Ias). Although nucleosynthesis constraints limit the number of neutron stars formed via AICs to <0.1% of the total galactic neutron star population, AICs remain a viable scenario for forming systems of neutron stars which are difficult to explain with Type II core-collapse supernovae.Comment: Latex File, aaspp4 style, 18 pages total (5 figures), accepted by Ap

Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies

BACKGROUND: Recent studies indicate that microRNAs (miRNAs) are mechanistically involved in the development of various human malignancies, suggesting that they represent a promising new class of cancer biomarkers. However, previously reported methods for measuring miRNA expression consume large amounts of tissue, prohibiting high-throughput miRNA profiling from typically small clinical samples such as excision or core needle biopsies of breast or prostate cancer. Here we describe a novel combination of linear amplification and labeling of miRNA for highly sensitive expression microarray profiling requiring only picogram quantities of purified microRNA. RESULTS: Comparison of microarray and qRT-PCR measured miRNA levels from two different prostate cancer cell lines showed concordance between the two platforms (Pearson correlation R(2 )= 0.81); and extension of the amplification, labeling and microarray platform was successfully demonstrated using clinical core and excision biopsy samples from breast and prostate cancer patients. Unsupervised clustering analysis of the prostate biopsy microarrays separated advanced and metastatic prostate cancers from pooled normal prostatic samples and from a non-malignant precursor lesion. Unsupervised clustering of the breast cancer microarrays significantly distinguished ErbB2-positive/ER-negative, ErbB2-positive/ER-positive, and ErbB2-negative/ER-positive breast cancer phenotypes (Fisher exact test, p = 0.03); as well, supervised analysis of these microarray profiles identified distinct miRNA subsets distinguishing ErbB2-positive from ErbB2-negative and ER-positive from ER-negative breast cancers, independent of other clinically important parameters (patient age; tumor size, node status and proliferation index). CONCLUSION: In sum, these findings demonstrate that optimized high-throughput microRNA expression profiling offers novel biomarker identification from typically small clinical samples such as breast and prostate cancer biopsies

Simulating the Common Envelope Phase of a Red Giant Using SPH and Uniform Grid Codes

We use three-dimensional hydrodynamical simulations to study the rapid infall phase of the common envelope interaction of a red giant branch star of mass equal to 0.88 \msun and a companion star of mass ranging from 0.9 down to 0.1 \msun. We first compare the results obtained using two different numerical techniques with different resolutions, and find overall very good agreement. We then compare the outcomes of those simulations with observed systems thought to have gone through a common envelope. The simulations fail to reproduce those systems in the sense that most of the envelope of the donor remains bound at the end of the simulations and the final orbital separations between the donor's remnant and the companion, ranging from 26.8 down to 5.9 \rsun, are larger than the ones observed. We suggest that this discrepancy vouches for recombination playing an essential role in the ejection of the envelope and/or significant shrinkage of the orbit happening in the subsequent phase.Comment: 45 pages, 19 figures, accepted to Ap

Potential of Notochordal Cells within Injectable Biomaterials to Promote Intervertebral Disc Regeneration

Low back pain is the leading cause of disability worldwide and is strongly associated with degeneration of the intervertebral disc (IVD).During degeneration the nucleus pulposus (NP) in the core of the IVD, is affected by altered matrix synthesis, increased degradation, andcell loss. Strategies combining regenerative cell sources with injectable biomaterials could provide a therapeutic approach to treatingIVD-degeneration related back pain. The juvenile cells of the NP, known as notochordal cells (NC), could provide both anabolic andanti-catabolic responses for disc regeneration. However, their behaviour within biomaterial delivery systems has not been investigated.Here, porcine NCs were incorporated into three injectable hydrogels: Albugel (an albumin/hyaluronan hydrogel), NPgel (a L-pNIPAMco-DMAc hydrogel) and NPgel with decellularized NC-matrix powder (dNCM). The NCs and biomaterial constructs were cultured for upto 4 weeks under 5% oxygen (n = 3 biological repeats). The ability of biomaterials to maintain NC viability, phenotype and extracellularmatrix synthesis and deposition was investigated through histological, immunohisto chemical and glycosaminogly cans analysis. NCs survived in all three biomaterials after 4 weeks, whilst phenotype and cell clustering were maintained to a greater extent in NPgel and Albugel. Thus, these biomaterials could facilitate maintenance of the NC phenotype, support matrix deposition and be a basis for future IVD regeneration strategies

Planetary population synthesis

In stellar astrophysics, the technique of population synthesis has been successfully used for several decades. For planets, it is in contrast still a young method which only became important in recent years because of the rapid increase of the number of known extrasolar planets, and the associated growth of statistical observational constraints. With planetary population synthesis, the theory of planet formation and evolution can be put to the test against these constraints. In this review of planetary population synthesis, we first briefly list key observational constraints. Then, the work flow in the method and its two main components are presented, namely global end-to-end models that predict planetary system properties directly from protoplanetary disk properties and probability distributions for these initial conditions. An overview of various population synthesis models in the literature is given. The sub-models for the physical processes considered in global models are described: the evolution of the protoplanetary disk, the planets' accretion of solids and gas, orbital migration, and N-body interactions among concurrently growing protoplanets. Next, typical population synthesis results are illustrated in the form of new syntheses obtained with the latest generation of the Bern model. Planetary formation tracks, the distribution of planets in the mass-distance and radius-distance plane, the planetary mass function, and the distributions of planetary radii, semimajor axes, and luminosities are shown, linked to underlying physical processes, and compared with their observational counterparts. We finish by highlighting the most important predictions made by population synthesis models and discuss the lessons learned from these predictions - both those later observationally confirmed and those rejected.Comment: 47 pages, 12 figures. Invited review accepted for publication in the 'Handbook of Exoplanets', planet formation section, section editor: Ralph Pudritz, Springer reference works, Juan Antonio Belmonte and Hans Deeg, Ed

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin