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

Scaling-up beginning farmers for wholesale production

With nearly 15 million people that live within 250 miles of Kansas City, the demand for local food is increasing. Local beginning farmers in the region want to reach an emerging wholesale market. However, selling directly to consumers demands different skills than the wholesale market requires. There are many educational programs offered in the region that are focused on direct to consumer sales. Unfortunately, there is a gap in educational programs that are offered to support beginning farmers that wish to expand into wholesale markets. In 2018, the Beginning Farmer Wholesale Project was started within the Growing Growers Kansas City program in congruence with the overall mission to improve the skills and livelihoods of the region’s growers. The project offers support and training to beginning farmers as they begin to navigate new market opportunities. It provides on-farm technical assistance, mentorship, opportunities to connect to wholesale buyers, a workshop series, a manual and an extensive foodshed GIS map. The ongoing project has seen several contributions to improving farmer access to wholesale markets. As of 2020, six workshops have been conducted that have covered a variety of farm production and marketing skills. Six farmer mentees have enrolled in the mentor program which enlists nine farmer mentors from across the region. Over twenty farmers have utilized the technical assistance service on their Kansas and Missouri farm operations and the farmer buyer matching program has resulted in thirteen beginning farmers gaining access to new markets. The project highlights the value of collaboration among organizations and the importance of offering multiple farmer services in order to improve wholesale access

A Simplified Cellular Automaton Model for City Traffic

We systematically investigate the effect of blockage sites in a cellular automaton model for traffic flow. Different scheduling schemes for the blockage sites are considered. None of them returns a linear relationship between the fraction of ``green'' time and the throughput. We use this information for a fast implementation of traffic in Dallas.Comment: 12 pages, 18 figures. submitted to Phys Rev

Noise effects in the quantum search algorithm from the computational complexity point of view

We analyse the resilience of the quantum search algorithm in the presence of quantum noise modelled as trace preserving completely positive maps. We study the influence of noise on computational complexity of the quantum search algorithm. We show that only for small amounts of noise the quantum search algorithm is still more efficient than any classical algorithm.Comment: 7 pages, 2 figure

Markovian MC simulation of QCD evolution at NLO level with minimum k_T

We present two Monte Carlo algorithms of the Markovian type which solve the modified QCD evolution equations at the NLO level. The modifications with respect to the standard DGLAP evolution concern the argument of the strong coupling constant alpha_S. We analyze the z - dependent argument and then the k_T - dependent one. The evolution time variable is identified with the rapidity. The two algorithms are tested to the 0.05% precision level. We find that the NLO corrections in the evolution of parton momentum distributions with k_T - dependent coupling constant are of the order of 10 to 20%, and in a small x region even up to 30%, with respect to the LO contributions.Comment: 32 pages, 9 pdf figure

kt - factorization and CCFM - the solution for describing the hadronic final states - everywhere ?

The basic ideas of kt-factorization and CCFM parton evolution is discussed. The unintegrated gluon densities, obtained from CCFM fits to the proton structure function data at HERA are used to predict hadronic final state cross sections like jet production at HERA, but also comparisons with recent measurements of heavy quark production at the Tevatron are presented. Finally, the kt-factorization approach is applied to Higgs production at high energy hadron hadron colliders and the transverse momentum spectrum of Higgs production at the LHC is calculated.Comment: to be published in MPLA, replaced with new reference

BET bromodomain inhibitors suppress inflammatory activation of gingival fibroblasts and epithelial cells from periodontitis patients

BET bromodomain proteins are important epigenetic regulators of gene expression that bind acetylated histone tails and regulate the formation of acetylation-dependent chromatin complexes. BET inhibitors suppress inflammatory responses in multiple cell types and animal models, and protect against bone loss in experimental periodontitis in mice. Here, we analyzed the role of BET proteins in inflammatory activation of gingival fibroblasts (GFs) and gingival epithelial cells (GECs). We show that the BET inhibitors I-BET151 and JQ1 significantly reduced expression and/or production of distinct, but overlapping, profiles of cytokine-inducible mediators of inflammation and bone resorption in GFs from healthy donors (IL6, IL8, IL1B, CCL2, CCL5, COX2, and MMP3) and the GEC line TIGK (IL6, IL8, IL1B, CXCL10, MMP9) without affecting cell viability. Activation of mitogen-activated protein kinase and nuclear factor-κB pathways was unaffected by I-BET151, as was the histone acetylation status, and new protein synthesis was not required for the anti-inflammatory effects of BET inhibition. I-BET151 and JQ1 also suppressed expression of inflammatory cytokines, chemokines, and osteoclastogenic mediators in GFs and TIGKs infected with the key periodontal pathogen Porphyromonas gingivalis. Notably, P. gingivalis internalization and intracellular survival in GFs and TIGKs remained unaffected by BET inhibitors. Finally, inhibition of BET proteins significantly reduced P. gingivalis-induced inflammatory mediator expression in GECs and GFs from patients with periodontitis. Our results demonstrate that BET inhibitors may block the excessive inflammatory mediator production by resident cells of the gingival tissue and identify the BET family of epigenetic reader proteins as a potential therapeutic target in the treatment of periodontal disease

Association of distinct fine specificities of anti-citrullinated peptide antibodies with elevated immune responses to Prevotella intermedia in a subgroup of patients with rheumatoid arthritis and periodontitis

Objective In addition to the long-established link with smoking, periodontitis (PD) is also a risk factor for rheumatoid arthritis (RA). To elucidate the mechanism by which PD could induce antibodies to citrullinated peptides (ACPA), we examine the antibody response to a novel citrullinated peptide from cytokeratin type I 13 identified in gingival crevicular fluid (GCF), and compare the response to 4 other citrullinated peptides in patients with RA, well-characterized for PD and smoking. Methods The citrullinomes of GCF and periodontal tissue from people with PD were mapped by mass spectrometry. Antibodies to citrullinated peptides from cytokeratin type I 13 (cCK13), tenascin-C (cTNC5), vimentin (cVIM), enolase (CEP-1) and fibrinogen β (cFIBβ) were examined by ELISA in patients with RA (n=287) and osteoarthritis (OA) (n=330), and cross-reactivity assessed by inhibition assays. Results A novel citrullinated peptide cCK13-1 (444TSNASGR-cit-TSDV-cit-RP458) identified in GCF, exhibited elevated antibody responses in RA patients (24%). Anti-cCK13-1 antibodies correlated with anti-cTNC5 antibodies, and absorption experiments confirmed this was not due to cross-reactivity. Only anti-cCK13-1 and anti-cTNC5 were associated with antibodies to the periodontal pathogen Prevotella intermedia (p=0.05 and p =0.001 respectively), but not with antibodies to Porphyromonas gingivalis arginine gingipains. Antibodies to CEP-1, cFIBβ and cVIM correlated with each other, and with smoking and shared epitope risk factors in RA. Conclusion This study identifies two groups of ACPA fine specificities associated with different RA risk factors; one predominantly linked to smoking and shared epitope, the other linking anti- cTNC5 and cCK13-1 to infection with the periodontal pathogen P. intermedia

Catalytic enantioselective syn hydration of enones in water using a DNA-based catalyst

The enantioselective addition of water to olefins in an aqueous environment is a common transformation in biological systems, but was beyond the ability of synthetic chemists. Here, we present the first examples of a non-enzymatic catalytic enantioselective hydration of enones, for which we used a catalyst that comprises a copper complex, based on an achiral ligand, non-covalently bound to (deoxy)ribonucleic acid, which is the only source of chirality present under the reaction conditions. The chiral β-hydroxy ketone product was obtained in up to 82% enantiomeric excess. Deuterium-labelling studies demonstrated that the reaction is diastereospecific, with only the syn hydration product formed. So far, this diastereospecific and enantioselective reaction had no equivalent in conventional homogeneous catalysis