Temperature-sensitive protein–DNA dimerizers

Programmable DNA-binding polyamides coupled to short peptides have led to the creation of synthetic artificial transcription factors. A hairpin polyamide-YPWM tetrapeptide conjugate facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. Such small molecules function as protein-DNA dimerizers that stabilize complexes at composite DNA binding sites. Here we investigate the role of the linker that connects the polyamide to the peptide. We find that a substantial degree of variability in the linker length is tolerated at lower temperatures. At physiological temperatures, the longest linker tested confers a "switch"-like property on the protein-DNA dimerizer, in that it abolishes the ability of the YPWM moiety to recruit the natural transcription factor to DNA. These observations provide design principles for future artificial transcription factors that can be externally regulated and can function in concert with the cellular regulatory circuitry

Impact of depth of response on survival in patients treated with cobimetinib ± vemurafenib: pooled analysis of BRIM-2, BRIM-3, BRIM-7 and coBRIM.

BackgroundThis pooled analysis investigated the prognostic value of depth of response in two cohorts of patients with BRAFV600-mutated metastatic melanoma treated with vemurafenib or cobimetinib plus vemurafenib.MethodsThe data were pooled from BRIM-2, BRIM-3, BRIM-7 and coBRIM. Association of depth of response with survival was estimated by Cox proportional hazards regression, adjusted for clinically relevant covariates. Depth of response was analysed in previously identified prognostic subgroups based on disease characteristics and gene signatures.ResultsGreater tumour reduction and longer time to maximal response were significantly associated with longer progression-free survival (PFS) and overall survival (OS) when evaluated as continuous variables. Patients with the deepest responses had long-lasting survival outcomes (median PFS: 14 months; OS: 32 months with vemurafenib; not estimable with cobimetinib plus vemurafenib). Cobimetinib plus vemurafenib improved depth of response versus vemurafenib monotherapy regardless of other prognostic factors, including gene signatures.ConclusionsGreater depth of response was associated with improved survival, supporting its utility as a measure of treatment efficacy in melanoma and further evaluation of its incorporation into existing prognostic models. Cobimetinib plus vemurafenib improved outcomes across quartiles of response regardless of prognostic factors or gene signatures and provided durable survival benefits in patients with deep responses

Toward artificial developmental regulators

A polyamide-peptide conjugate is designed which recruits sequence specifically the developmental regulator Exd to a cognate DNA site. In particular, an eight-ring hairpin polyamide (Im-Im-Py(C3H6NHR)-Py-gamma-Im-Py-Py-Py-beta-Dp) with a heptapeptide (R = Ac-Phe-Tyr-Pro-Trp-Met-Lys-Gly-) attached on a central ring was shown to induce cooperative binding of the Drosophila Hox protein cofactor Exd with a Kd of 4.4 nM in vitro, an order of magnitude more efficient than the natural Hox protein partner Ubx. The conjugate joins two sequence specific domains, one for DNA and one for the protein. This small molecule thus serves as a cooperative protein-DNA dimerizer, which mimics the natural Hox family of developmental regulators

Pharmacokinetic study on pradofloxacin in the dog – Comparison of serum analysis, ultrafiltration and tissue sampling after oral administration

Background: Pradofloxacin, a newly developed 8-cyano-fluoroquinolone, show enhanced activity against Grampositive organisms and anaerobes to treat canine and feline bacterial infections. The purpose of this cross-over study was to measure the unbound drug concentration of pradofloxacin in the interstitial fluid (ISF) using ultrafiltration and to compare the kinetics of pradofloxacin in serum, ISF and tissue using enrofloxacin as reference. Results: After oral administration of enrofloxacin (5 mg/kg) and pradofloxacin (3 mg/kg and 6 mg/kg, respectively), serum collection and ultrafiltration in regular intervals over a period of 24 h were performed, followed by tissue sampling at the end of the third dosing protocol (pradofloxacin 6 mg/kg). Peak concentrations of pradofloxacin (3 mg/kg) were 1.55±0.31 μg/ml in the ISF and 1.85±0.23 μg/ml in serum and for pradofloxacin (6 mg/kg) 2.71±0.81 μg/kg in the ISF and 2.77±0.64 μg/kg in serum; both without a statistical difference between ISF and serum. Comparison between all sampling approaches showed no consistent pattern of statistical differences. Conclusions: Despite some technical shortcomings the ultrafiltration approach appears to be the most sensitive sampling technique to estimate pharmacokinetic values of pradofloxacin at the infection site. Pharmacokinetics – Pradofloxacin – Ultrafiltration – Dog – Oral Administration

DFG-Forschungsprojekt "Krustensplitter" : 3D-Makro-Geschwindigkeitsbestimmungen und 3D-Tiefenmigration des seismischen 3D-Costa-Rica-Datensatzes

Thema des Gemeinschaftsprojektes: Dreidimensionale Detailabbildungen prominenter reflexionsseismischer Strukturen am aktiven Kontinentalrand vor Costa Rica Förderungszeitraum insgesamt vom 01.07.1996 bis 31.12.199

Toward artificial developmental regulators

A polyamide-peptide conjugate is designed which recruits sequence specifically the developmental regulator Exd to a cognate DNA site. In particular, an eight-ring hairpin polyamide (Im-Im-Py(C3H6NHR)-Py-gamma-Im-Py-Py-Py-beta-Dp) with a heptapeptide (R = Ac-Phe-Tyr-Pro-Trp-Met-Lys-Gly-) attached on a central ring was shown to induce cooperative binding of the Drosophila Hox protein cofactor Exd with a Kd of 4.4 nM in vitro, an order of magnitude more efficient than the natural Hox protein partner Ubx. The conjugate joins two sequence specific domains, one for DNA and one for the protein. This small molecule thus serves as a cooperative protein-DNA dimerizer, which mimics the natural Hox family of developmental regulators

Gas inflows in the polar ring of NGC 4111 : the birth of an AGN

We have used Hubble Space Telescope (HST) images, SAURON Integral Field Spectroscopy (IFS), and adaptative optics assisted Gemini NIFS near-infrared K-band IFS to map the stellar and gas distribution, excitation and kinematics of the inner few kpc of the nearby edge-on S0 galaxy NGC 4111. The HST images map its ≈450 pc diameter dusty polar ring, with an estimated gas mass ≥107 M . The NIFS data cube maps the inner 110 pc radius at ≈7 pc spatial resolution, revealing a ≈220 pc diameter polar ring in hot (2267 ± 166 K) molecular H2 1–0 S(1) gas embedded in the polar ring. The stellar velocity field shows disc-dominated kinematics along the galaxy plane both in the SAURON large scale and in the NIFS nuclear-scale data. The large-scale [O III] λ5007 Å velocity field shows a superposition of two disc kinematics: one similar to that of the stars and another along the polar ring, showing non-circular motions that seem to connect with the velocity field of the nuclear H2 ring, whose kinematics indicate accelerated inflow to the nucleus. The estimated mass inflow rate is enough not only to feed an active galactic nucleus (AGN) but also to trigger circumnuclear star formation in the near future. We propose a scenario in which gas from the polar ring, which probably originated from the capture of a dwarf galaxy, is moving inwards and triggering an AGN, as supported by the local X-ray emission, which seems to be the source of the H2 1–0 S(1) excitation. The fact that we see neither near-UV nor Br γ emission suggests that the nascent AGN is still deeply buried under the optically thick dust of the polar ring

Gas inflows in the polar ring of NGC 4111: the birth of an AGN

We have used Hubble Space Telescope (HST) images, SAURON Integral Field Spectroscopy (IFS) and adaptative optics assisted Gemini NIFS near-infrared K-band IFS to map the stellar and gas distribution, excitation and kinematics of the inner few kpc of the nearby edge-on S0 galaxy NGC 4111. The HST images map its $\approx$ 450 pc diameter dusty polar ring, with an estimated gas mass $\ge10^7$ M$_\odot$. The NIFS datacube maps the inner 110 pc radius at $\approx$ 7 pc spatial resolution revealing a $\approx$ 220 pc diameter polar ring in hot ($2267\pm166$ K) molecular H$_2$ 1-0 S(1) gas embedded in the polar ring. The stellar velocity field shows disk-dominated kinematics along the galaxy plane both in the SAURON large-scale and in the NIFS nuclear-scale data. The large-scale [O III] $\lambda5007$ \AA velocity field shows a superposition of two disk kinematics: one similar to that of the stars and another along the polar ring, showing non-circular motions that seem to connect with the velocity field of the nuclear H$_2$ ring, whose kinematics indicate accelerated inflow to the nucleus. The estimated mass inflow rate is enough not only to feed an Active Galactic Nucleus (AGN) but also to trigger circumnuclear star formation in the near future. We propose a scenario in which gas from the polar ring, which probably originated from the capture of a dwarf galaxy, is moving inwards and triggering an AGN, as supported by the local X-ray emission, which seems to be the source of the H$_2$ 1-0 S(1) excitation. The fact that we see neither near-UV nor Br$\gamma$ emission suggests that the nascent AGN is still deeply buried under the optically thick dust of the polar ring.Comment: 18 pages, 21 figure