Reverse engineering of drug induced DNA damage response signalling pathway reveals dual outcomes of ATM kinase inhibition

The DNA Damage Response (DDR) pathway represents a signalling mechanism that is activated in eukaryotic cells following DNA damage and comprises of proteins involved in DNA damage detection, DNA repair, cell cycle arrest and apoptosis. This pathway consists of an intricate network of signalling interactions driving the cellular ability to recognise DNA damage and recruit specialised proteins to take decisions between DNA repair or apoptosis. ATM and ATR are central components of the DDR pathway. The activities of these kinases are vital in DNA damage induced phosphorylational induction of DDR substrates. Here, firstly we have experimentally determined DDR signalling network surrounding the ATM/ATR pathway induced following double stranded DNA damage by monitoring and quantifying time dependent inductions of their phosphorylated forms and their key substrates. We next involved an automated inference of unsupervised predictive models of time series data to generate in silico (molecular) interaction maps. We characterized the complex signalling network through system analysis and gradual utilisation of small time series measurements of key substrates through a novel network inference algorithm. Furthermore, we demonstrate an application of an assumption-free reverse engineering of the intricate signalling network of the activated ATM/ATR pathway. We next studied the consequences of such drug induced inductions as well as of time dependent ATM kinase inhibition on cell survival through further biological experiments. Intermediate and temporal modelling outcomes revealed the distinct signaling profile associated with ATM kinase activity and inhibition and explained the underlying signalling mechanism for dual ATM functionality in cytotoxic and cytoprotective pathways

Understanding tissue morphology: model repurposing using the CoSMoS process

We present CoSMoS as a way of structuring thinking on how to reuse parts of an existing model and simulation in a new model and its implementation. CoSMoS provides a lens through which to consider, post-implementation, the assumptions made during the design and implementation of a software simulation of physical interactions in the formation of vascular structures from endothelial cells. We show how the abstract physical model and its software implementation can be adapted for a different problem: the growth of cancer cells under varying environmental perturbations. We identify the changes that must be made to adapt the model to its new context, along with the gaps in our knowledge of the domain that must be filled by wet-lab experimentation when recalibrating the model. Through parameter exploration, we identify the parameters that are critical to the dynamic physical structure of the modelled tissue, and we calibrate these parameters using a series of in vitro experiments. Drawing inspiration from the CoSMoS project structure, we maintain confidence in the repurposed model, and achieve a satisfactory degree of model reuse within our in silico experimental system

NRF2 regulates HER1 signaling pathway to modulate the sensitivity of ovarian cancer cells to lapatinib and erlotinib

NF-E2-related factor 2 (NRF2) regulates the transcription of a battery of metabolic and cytoprotective genes. NRF2 and epidermal growth factor receptors (EGFRs/HERs) are regulators of cellular proliferation and determinants of cancer initiation and progression. NRF2 and HERs confer cancers with resistance to several therapeutic agents. Nevertheless, there is limited understanding of the regulation of HER expression and activation and the link between NRF2 and HER signalling pathways. We show that NRF2 regulates both basal and inducible expression of HER1, as treatment of ovarian cancer cells (PEO1, OVCAR3, and SKOV3) with NRF2 activator tBHQ inducing HER1, while inhibition of NRF2 by siRNA knockdown or with retinoid represses HER1. Furthermore, treatment of cells with tBHQ increased total and phosphorylated NRF2, HER1, and AKT levels and compromised the cytotoxic effect of lapatinib or erlotinib. Treatment with siRNA or retinoid antagonised the effect of tBHQ on NRF2 and HER1 levels and enhanced the sensitivity of ovarian cancer cells to lapatinib or erlotinib. Pharmacological or genetic inhibition of NRF2 and/or treatment with lapatinib or erlotinib elevated cellular ROS and depleted glutathione. This extends the understanding of NRF2 and its regulation of HER family receptors and opens a strategic target for improving cancer therapy

Effect of Solid Particle Properties on Heat Transfer and Pressure Drop in Packed Duct

This work examines numerically the effects of particle size, particle thermal conductivity and inlet velocity of forced convection heat transfer in uniformly heated packed duct. Four packing material (Aluminum, Alumina, Glass and Nylon) with range of thermal conductivity (from200 W/m.K for Aluminum to 0.23 W/m.K for Nylon), four particle diameters (1, 3, 5 and 7 cm), inlet velocity ( 0.07, 0.19 and 0.32 m/s) and constant heat flux ( 1000, 2000 and 3000 W/ m 2) were investigated. Results showed that heat transfer (average Nusselt number Nuav) increased with increasing packing conductivity; inlet velocity and heat flux, but decreased with increasing particle size.Also, Aluminum average Nusselt number is about (0.85,2.2 and 3.1 times) than Alumina, glass and Nylon respectively. From optimization between heat transfer and pressure drop through packed duct, it is found thatfinest ratio (Nuav / ?p) equal to (19.12) at (Dp = 7 cm, inlet velocity = 0.07 m/ s and 3000 W/m2 heat flux) with Aluminum as packing material

Gamma-D crystallin gene (CRYGD) mutation causes autosomal dominant congenital cerulean cataracts

Congenital cataracts are a major cause of bilateral visual impairment in childhood. We mapped the gene responsible for autosomal congenital cerulean cataracts to chromosome 2q33-35 in a four generation family of Moroccan descent. The maximum lod score (7.19 at recombination fraction theta=0) was obtained for marker D2S2208 near the g-crystallin gene (CRYG) cluster. Sequencing of the coding regions of the CRYGA, B, C, and D genes showed the presence of a heterozygous C>A transversion in exon 2 of CRYGD that is associated with cataracts in this family. This mutation resulted in a proline to threonine substitution at amino acid 23 of the protein in the first of the four Greek key motifs that characterise this protein. We show that although the x ray crystallography modelling does not indicate any change of the backbone conformation, the mutation affects a region of the Greek key motif that is important for determining the topology of this protein fold. Our data suggest strongly that the proline to threonine substitution may alter the protein folding or decrease the thermodynamic stability or solubility of the protein. Furthermore, this is the first report of a mutation in this gene resulting in autosomal dominant congenital cerulean cataracts

Systems analysis of drug-induced receptor tyrosine kinase reprogramming following targeted mono- and combination anti-cancer therapy

The receptor tyrosine kinases (RTKs) are key drivers of cancer progression and targets for drug therapy. A major challenge in anti-RTK treatment is the dependence of drug effectiveness on co-expression of multiple RTKs which defines resistance to single drug therapy. Reprogramming of the RTK network leading to alteration in RTK co-expression in response to drug intervention is a dynamic mechanism of acquired resistance to single drug therapy in many cancers. One route to overcome this resistance is combination therapy. We describe the results of a joint in silico, in vitro, and in vivo investigations on the efficacy of trastuzumab, pertuzumab and their combination to target the HER2 receptors. Computational modelling revealed that these two drugs alone and in combination differentially suppressed RTK network activation depending on RTK co-expression. Analyses of mRNA expression in SKOV3 ovarian tumour xenograft showed up-regulation of HER3 following treatment. Considering this in a computational model revealed that HER3 up-regulation reprograms RTK kinetics from HER2 homodimerisation to HER3/HER2 heterodimerisation. The results showed synergy of the trastuzumab and pertuzumab combination treatment of the HER2 overexpressing tumour can be due to an independence of the combination effect on HER3/HER2 composition when it changes due to drug-induced RTK reprogramming

A Numerical Analysis of Shock Angles from Inward Turning Axisymmetric Flows

Detonation-based propulsion systems are known for their high efficiency and energy release when compared to deflagrative systems, making them an ideal candidate in hypersonic propulsion applications. One such engine is the Oblique Detonation Wave (ODW) engine, which has a similar architecture to traditional scramjets but shortens the combustor and isolator to an anchored ODW after fuel injection. Previous research has focused on using a two-dimensional wedge to induce an ODW while limiting total losses through the combustor. In this configuration, a two-dimensional wedge-based architecture entails a rectangular duct, limiting potential inlet design and increasing overall skin friction. However, an inward-turning axisymmetric ODW wedge architecture, where a two-dimensional wedge is revolved around a central axis, has yet to be examined in detail. The work at present aims to investigate the fundamental physics required to predict the Oblique Shock Wave (OSW) for an inward-turning axisymmetric flow, which is critical for designing a circular ODW engine combustor. Multiple steady simulations of inviscid and ideal air at Mach 4, 6, and 8 were performed over a 1-inch wedge with wedge angles of 16°, 18°, and 20°. The radius of the inlet boundary was also varied between 1, 3, and 5 inches to examine the effect of increasing the blockage ratio. The results showed that the shock angle for an inward-turning axisymmetric flow was up to 8% steeper than the analytical, two-dimensional wedge solution. Additionally, it was found that the OSW diverged further from the two-dimensional solution when the blockage ratio was increased. These findings provide insight into the flow physics that must be considered when designing inward-turning axisymmetric ODW engines

Batum; in the First World War and Turkish National War of Independence

DergiPark: 326543trakyasobedof the Bolsheviks in Russia -and their eventual hold of the government- has given the Ottoman Empire theopportunity to have Kars, Ardahan and Batum back to her control. During the Turkish National War of Independence, Batum became a significant area of maneuver for the new National Assembly’s (TBMM) foreign policy. The main aim of TBMM’s foreign politics was partly to re-balance the power gap between the two sides of the War of Independence. In this frame, gaining the support of a “big state” appeared as a strategic goal which was perennial to the success of the cause. Obviously, the state of the international relations of the era permitted this “big state” to be no other then the USSR. TBMM didn’t hesitate to leave Batum as a concession to USSR to strengthen the bi-lateral relations through gaining the trust of the Bolsheviks. When judged by the outcome, the consequent events strongly indicate that, this strategy has handsomely paid of and, in time, the handing over of the Batum to the USSR proves to be an act of clever real-politics, which brought strategic profundity to the Turkish foreign policy rather than a lossBatum, Osmanlı Devleti’nin ağır bir yenilgi aldığı 1877 – 1878 Osmanlı – Rus Savaşı’nın sonunda imzalanan Ayastafenos Anlaşması’nın hükümleri gereğince Kars ve Ardahan’la birlikte Rusya’ya bırakıldı. Osmanlı Devleti, I. Dünya Savaşı sırasında Kafkas cephesinde düzenlediği harekatla buraların yeniden Osmanlı topraklarına katılmasını hedefledi. Ancak Kafkas cephesinde hiçbir şey yolunda gitmedi; Osmanlı Devleti buraları almak bir yana, Doğu Anadolu’nun önemli bir bölümünü Ruslara teslim etti. Rusya’da Bolşeviklerin iktidarı ele geçirmesine koşut yaşanan gelişmelerse Ardahan ve Kars’la birlikte Batum’un da yeniden Osmanlı topraklarına katılmasını sağladı. Batum, bundan sonraki dönemde Türk Ulusal Bağımsızlık Savaşımı sırasında TBMM’nin izlediği dış politikayı yakından ilgilendiren bir bölge olarak anlam kazandı. TBMM’nin bu dönemdeki dış politikasının amacı, büyük ölçüde, savaşan taraflar arasındaki güç dengesizliğini gidermeye yönelikti. Bu çerçeve içinde, bir büyük devletin desteğini kazanabilmek önemli bir hedef olarak belirdi. Bu “büyük devlet” o günün koşulları içinde, kuşkusuz, SSCB’den başkası olamazdı. TBMM, SSCB’nin desteğini sağlayabilmek adına, Batum’u bir ödün niteliğinde SSCB’ye bırakmaktan çekinmedi. İzleyen gelişmelere bakıldığında bu stratejinin önemli ölçüde olumlu sonuç verdiği görülmektedir. Bu anlamda Batum’un SSCB’ye terk edilmesi, kayba yol açan bir hatadan çok; Türk dış politikasına stratejik derinlik sağlayan akıllıca bir gerçekçi siyaset eylemi niteliğindedi

Fast Optimal Locally Private Mean Estimation via Random Projections

We study the problem of locally private mean estimation of high-dimensional vectors in the Euclidean ball. Existing algorithms for this problem either incur sub-optimal error or have high communication and/or run-time complexity. We propose a new algorithmic framework, ProjUnit, for private mean estimation that yields algorithms that are computationally efficient, have low communication complexity, and incur optimal error up to a $1+o(1)$-factor. Our framework is deceptively simple: each randomizer projects its input to a random low-dimensional subspace, normalizes the result, and then runs an optimal algorithm such as PrivUnitG in the lower-dimensional space. In addition, we show that, by appropriately correlating the random projection matrices across devices, we can achieve fast server run-time. We mathematically analyze the error of the algorithm in terms of properties of the random projections, and study two instantiations. Lastly, our experiments for private mean estimation and private federated learning demonstrate that our algorithms empirically obtain nearly the same utility as optimal ones while having significantly lower communication and computational cost.Comment: Added the correct github lin