A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics.

Synthetic protein switches controlled with user-defined inputs are powerful tools for studying and controlling dynamic cellular processes. To date, these approaches have relied primarily on intermolecular regulation. Here we report a computationally guided framework for engineering intramolecular regulation of protein function. We utilize this framework to develop chemically inducible activator of RAS (CIAR), a single-component RAS rheostat that directly activates endogenous RAS in response to a small molecule. Using CIAR, we show that direct RAS activation elicits markedly different RAS-ERK signaling dynamics from growth factor stimulation, and that these dynamics differ among cell types. We also found that the clinically approved RAF inhibitor vemurafenib potently primes cells to respond to direct wild-type RAS activation. These results demonstrate the utility of CIAR for quantitatively interrogating RAS signaling. Finally, we demonstrate the general utility of our approach in design of intramolecularly regulated protein tools by applying it to the Rho family of guanine nucleotide exchange factors

Expression of Drug Targets in Patients Treated with Sorafenib, Carboplatin and Paclitaxel

Introduction: Sorafenib, a multitarget kinase inhibitor, targets members of the mitogen-activated protein kinase (MAPK) pathway and VEGFR kinases. Here we assessed the association between expression of sorafenib targets and biomarkers of taxane sensitivity and response to therapy in pre-treatment tumors from patients enrolled in ECOG 2603, a phase III comparing sorafenib, carboplatin and paclitaxel (SCP) to carboplatin, paclitaxel and placebo (CP). Methods: Using a method of automated quantitative analysis (AQUA) of in situ protein expression, we quantified expression of VEGF-R2, VEGF-R1, VEGF-R3, FGF-R1, PDGF-Rβ, c-Kit, B-Raf, C-Raf, MEK1, ERK1/2, STMN1, MAP2, EB1 and Bcl-2 in pretreatment specimens from 263 patients. Results: An association was found between high FGF-R1 and VEGF-R1 and increased progression-free survival (PFS) and overall survival (OS) in our combined cohort (SCP and CP arms). Expression of FGF-R1 and VEGF-R1 was higher in patients who responded to therapy ((CR+PR) vs. (SD+PD+ un-evaluable)). Conclusions: In light of the absence of treatment effect associated with sorafenib, the association found between FGF-R1 and VEGF-R1 expression and OS, PFS and response might reflect a predictive biomarker signature for carboplatin/paclitaxel-based therapy. Seeing that carboplatin and pacitaxel are now widely used for this disease, corroboration in another cohort might enable us to improve the therapeutic ratio of this regimen. © 2013 Jilaveanu et al

Theory of Banana Liquid Crystal Phases and Phase Transitions

We study phases and phase transitions that can take place in the newly discovered banana (bow-shaped or bent-core) liquid crystal molecules. We show that to completely characterize phases exhibited by such bent-core molecules a third-rank tensor $T^{ijk}$ order parameter is necessary in addition to the vector and the nematic (second-rank) tensor order parameters. We present an exhaustive list of possible liquid phases, characterizing them by their space-symmetry group and order parameters, and catalog the universality classes of the corresponding phase transitions that we expect to take place in such bent-core molecular liquid crystals. In addition to the conventional liquid-crystal phases such as the nematic phase, we predict the existence of novel liquid phases, including the spontaneously chiral nematic $(N_T + 2)^*$ and chiral polar $(V_T + 2)^*$ phases, the orientationally-ordered but optically isotropic tetrahedratic $T$ phase, and a novel nematic $N_T$ phase with $D_{2d}$ symmetry that is neither uniaxial nor biaxial. Interestingly, the Isotropic-Tetrahedratic transition is {\em continuous} in mean-field theory, but is likely driven first-order by thermal fluctuations. We conclude with a discussion of smectic analogs of these phases and their experimental signatures.Comment: 28 pgs. RevTex, 32 eps figures, submitted to Phys. Rev.

Considering the Case for Biodiversity Cycles: Reexamining the Evidence for Periodicity in the Fossil Record

Medvedev and Melott (2007) have suggested that periodicity in fossil biodiversity may be induced by cosmic rays which vary as the Solar System oscillates normal to the galactic disk. We re-examine the evidence for a 62 million year (Myr) periodicity in biodiversity throughout the Phanerozoic history of animal life reported by Rohde & Mueller (2005), as well as related questions of periodicity in origination and extinction. We find that the signal is robust against variations in methods of analysis, and is based on fluctuations in the Paleozoic and a substantial part of the Mesozoic. Examination of origination and extinction is somewhat ambiguous, with results depending upon procedure. Origination and extinction intensity as defined by RM may be affected by an artifact at 27 Myr in the duration of stratigraphic intervals. Nevertheless, when a procedure free of this artifact is implemented, the 27 Myr periodicity appears in origination, suggesting that the artifact may ultimately be based on a signal in the data. A 62 Myr feature appears in extinction, when this same procedure is used. We conclude that evidence for a periodicity at 62 Myr is robust, and evidence for periodicity at approximately 27 Myr is also present, albeit more ambiguous.Comment: Minor modifications to reflect final published versio

The Grizzly, October 25, 1985

Registration has Come Upon Us • RA Supervision Allows Reimert\u27s Co-ed Transition • Siblings Sharing the Same Experience • One Hundred Years of Tradition Passes With Fretz • Prof. Profile: Armstrong Balances his own Studies With Students\u27 Studies • In Search of Success: Lehman Leans Towards Stockbroker • Letters: What is That Eye Material?; Walter Still Upset; Music Comes to UC • Scram Leaves its Name in Reimert History • Concert Review: Bon Jovi and Ratt Draw a Crowd of Leather • Wanted: Attempted Murder • Bears Fall to Fifth Ranked Gettysburg • Annual Snell Game Ends in a Tie • Booters Win a Big One Over Haverford Squad • Mers Ready to Plunge Into Season • New Course at U.C.: Human Sexuality • Richter Named as Chairman • How to Handle the Effects of Harmful Stress • Roving Reporter: Do You Think Fraternities and Sororities are a Positive Aspect of Campus Life?https://digitalcommons.ursinus.edu/grizzlynews/1149/thumbnail.jp

Markov Chain Monte Carlo and the Application to Geodetic Time Series Analysis

The time evolution of geophysical phenomena can be characterised by stochastic time series. The stochastic nature of the signal stems from the geophysical phenomena involved and any noise, which may be due to, e.g., un-modelled effects or measurement errors. Until the 1990's, it was usually assumed that white noise could fully characterise this noise. However, this was demonstrated to be not the case and it was proven that this assumption leads to underestimated uncertainties of the geophysical parameters inferred from the geodetic time series. Therefore, in order to fully quantify all the uncertainties as robustly as possible, it is imperative to estimate not only the deterministic but also the stochastic parameters of the time series. In this regard, the Markov Chain Monte Carlo (MCMC) method can provide a sample of the distribution function of all parameters, including those regarding the noise, e.g., spectral index and amplitudes. After presenting the MCMC method and its implementation in our MCMC software we apply it to synthetic and real time series and perform a cross-evaluation using Maximum Likelihood Estimation (MLE) as implemented in the CATS software. Several examples as to how the MCMC method performs as a parameter estimation method for geodetic time series are given in this chapter. These include the applications to GPS position time series, superconducting gravity time series and monthly mean sea level (MSL) records, which all show very different stochastic properties. The impact of the estimated parameter uncertainties on sub-sequentially derived products is briefly demonstrated for the case of plate motion models. Finally, the MCMC results for weekly downsampled versions of the benchmark synthetic GNSS time series as provided in Chapter 2 are presented separately in an appendix

The Grizzly, March 7, 1986

Meyer to Undergo Surgery • Teachers Always Looking to the Future: NASA Finalists Speak to Some U.C. Students • Garbage: It\u27s Expensive Stuff • Letters: CAB Responds to Only at Ursinus Comments; Student Offended by Walkman Listener at Haydn Concert • Bomberger Concerts Deserve Crowd, Too • Tie for First in Air Band • How to get that \u27A\u27 • It\u27s All in Good Fun Guys • What are You Doing Next Week? • Nuclear War as a Just War • Women\u27s Studies Offered in Fall • Mer Chicks a Success at MAC\u27s • U.C. Boys Bearing Down • Women\u27s Lacrosse Preview • Coach Brown Named Ass\u27t Athletic Director • Townshend Strikes Gold With White City LP • Tolkien Collection On Display in Myrin • Faculty Views of Pledginghttps://digitalcommons.ursinus.edu/grizzlynews/1160/thumbnail.jp