Alkyl-π engineering in state control toward versatile optoelectronic soft materials

Organic π-conjugated molecules with extremely rich and tailorable electronic and optical properties are frequently utilized for the fabrication of optoelectronic devices. To achieve high solubility for facile solution processing and desirable softness for flexible device fabrication, the rigid π units were in most cases attached by alkyl chains through chemical modification. Considerable numbers of alkylated-π molecular systems with versatile applications have been reported. However, a profound understanding of the molecular state control through proper alkyl chain substitution is still highly demanded because effective applications of these molecules are closely related to their physical states. To explore the underlying rule, we review a large number of alkylated-π molecules with emphasis on the interplay of van der Waals interactions (vdW) of the alkyl chains and π–π interactions of the π moieties. Based on our comprehensive investigations of the two interactions’ impacts on the physical states of the molecules, a clear guidance for state control by alkyl-π engineering is proposed. Specifically, either with proper alkyl chain substitution or favorable additives, the vdW and π–π interactions can be adjusted, resulting in modulation of the physical states and optoelectronic properties of the molecules. We believe the strategy summarized here will significantly benefit the alkyl-π chemistry toward wide-spread applications in optoelectronic devices.     

Anatomy of a negative feedback loop: the case of IκBα

The magnitude, duration and oscillation of cellular signalling pathway responses are often limited by negative feedback loops, defined as an ‘activator-induced inhibitor’ regulatory motif. Within the NFκB signalling pathway, a key negative feedback regulator is IκBα. We show here that, contrary to current understanding, NFκB-inducible expression is not sufficient for providing effective negative feedback. We then employ computational simulations of NFκB signalling to identify IκBα molecular properties that are critical for proper negative feedback control and test the resulting predictions in biochemical and single-cell live-imaging studies. We identified nuclear import and nuclear export of IκBα and the IκBα–NFκB complex, as well as the free IκBα half-life, as key determinants of post-induction repression of NFκB and the potential for subsequent reactivation. Our work emphasizes that negative feedback is an emergent systems property determined by multiple molecular and biophysical properties in addition to the required ‘activator-induced inhibitor’ relationship.     

Lifetime Measurements in 178Hf

Lifetimes of levels from K^π = 2⁺, K^π = 4⁺ and several K^π = 0⁺ bands have been measured in the ¹⁷⁸Hf nucleus using the GRID technique. Lifetimes of the 2⁺ and 3⁺ levels were measured within the K^π = 2⁺ γ band. A lower limit was established for the lifetime of the 4⁺ level of the K^π = 4⁺ band. The resulting upper limits for the absolute B(E2) values exclude collective transitions from the K^π = 4⁺ to the ground state band but not to the K^π= 2⁺ band. Level lifetimes were also measured for several states within three separate K^π= 0⁺ bands. Evidence is presented for a previously unobserved case of two excited K^π= 0⁺ bands being connected via collective E2 transitions.     

Intrinsic frequency for a systems approach to haemodynamic waveform analysis with clinical applications

The reductionist approach has dominated the fields of biology and medicine for nearly a century. Here, we present a systems science approach to the analysis of physiological waveforms in the context of a specific case, cardiovascular physiology. Our goal in this study is to introduce a methodology that allows for novel insight into cardiovascular physiology and to show proof of concept for a new index for the evaluation of the cardiovascular system through pressure wave analysis. This methodology uses a modified version of sparse time–frequency representation (STFR) to extract two dominant frequencies we refer to as intrinsic frequencies (IFs; ω₁ and ω₂). The IFs are the dominant frequencies of the instantaneous frequency of the coupled heart + aorta system before the closure of the aortic valve and the decoupled aorta after valve closure. In this study, we extract the IFs from a series of aortic pressure waves obtained from both clinical data and a computational model. Our results demonstrate that at the heart rate at which the left ventricular pulsatile workload is minimized the two IFs are equal (ω₁ = ω₂). Extracted IFs from clinical data indicate that at young ages the total frequency variation (Δω = ω₁ − ω₂) is close to zero and that Δω increases with age or disease (e.g. heart failure and hypertension). While the focus of this paper is the cardiovascular system, this approach can easily be extended to other physiological systems or any biological signal.     

Petri Net modelling approach for analysing the behaviour of Wnt/ β ‐catenin and Wnt/ Ca2+ signalling pathways in arrhythmogenic right ventricular cardiomyopathy

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease that may result in arrhythmia, heart failure and sudden death. The hallmark pathological findings are progressive myocyte loss and fibro fatty replacement, with a predilection for the right ventricle. This study focuses on the adipose tissue formation in cardiomyocyte by considering the signal transduction pathways including Wnt/ β ‐catenin and Wnt/Ca²⁺ regulation system. These pathways are modelled and analysed using stochastic petri nets (SPN) in order to increase our comprehension of ARVC and in turn its treatment regimen. The Wnt/ β ‐catenin model predicts that the dysregulation or absence of Wnt signalling, inhibition of dishevelled and elevation of glycogen synthase kinase 3 along with casein kinase I are key cytotoxic events resulting in apoptosis. Moreover, the Wnt/Ca²⁺ SPN model demonstrates that the Bcl2 gene inhibited by c‐Jun N‐terminal kinase protein in the event of endoplasmic reticulum stress due to action potential and increased amount of intracellular Ca²⁺ which recovers the Ca²⁺ homeostasis by phospholipase C, this event positively regulates the Bcl2 to suppress the mitochondrial apoptosis which causes ARVC.Inspec keywords: molecular biophysics, enzymes, cancer, muscle, Petri nets, cellular biophysics, bioelectric potentials, biomembranes, tumours, cardiology, genetics, biochemistry, calciumOther keywords: heart failure, sudden death, hallmark pathological findings, progressive myocyte loss, fibro fatty replacement, adipose tissue formation, signal transduction pathways, Ca²⁺ regulation system, stochastic petri nets, ARVC, $β‐catenin model, Wnt signalling, glycogen synthase kinase 3, Bcl2 gene, c‐Jun N‐terminal kinase protein, petri Net modelling approach, Ca²⁺ signalling pathways, arrhythmogenic right ventricular cardiomyopathy, inherited heart muscle disease, Ca²⁺ SPN model, Ca     

Multistability of signal transduction motifs

Protein domains are the basic units of signalling processes. The mechanisms they are involved in usually follow recurring patterns, such as phosphorylation/dephosphorylation cycles. A set of common motifs was defined and their dynamic models were analysed with respect to number and stability of steady states. In a first step, Feinberg's chemical reaction network theory was used to determine whether a motif can show multistationarity or not. The analysis revealed that, apart from double-step activation motifs including a distributive mechanism, only those motifs involving an autocatalytic reaction can show multistationarity. To further characterise these motifs, a large number of randomly chosen parameter sets leading to bistability was generated, followed by a bifurcation analysis of each parameter set and a statistical evaluation of the results. The statistical results can be used to explore robustness against noise, pointing to the observation that multistationarity at the single-motif level may not be a robust property; the range of protein concentrations compatible with multistationarity is fairly narrow. Furthermore, experimental evidence suggests that protein concentrations vary substantially between cells. Considering a motif designed to be a bistable switch, this implies that fluctuation of protein concentrations between cells would prevent a significant proportion of motifs from acting as a switch. The authors consider this to be a first step towards a catalogue of fully characterised signalling modules.     

Signalling pathway impact analysis based on the strength of interaction between genes

Signalling pathway analysis is a popular approach that is used to identify significant cancer‐related pathways based on differentially expressed genes (DEGs) from biological experiments. The main advantage of signalling pathway analysis lies in the fact that it assesses both the number of DEGs and the propagation of signal perturbation in signalling pathways. However, this method simplifies the interactions between genes by categorising them only as activation (+1) and suppression (−1), which does not encompass the range of interactions in real pathways, where interaction strength between genes may vary. In this study, the authors used newly developed signalling pathway impact analysis (SPIA) methods, SPIA based on Pearson correlation coefficient (PSPIA), and mutual information (MSPIA), to measure the interaction strength between pairs of genes. In analyses of a colorectal cancer dataset, a lung cancer dataset, and a pancreatic cancer dataset, PSPIA and MSPIA identified more candidate cancer‐related pathways than were identified by SPIA. Generally, MSPIA performed better than PSPIA.Inspec keywords: genetics, cancer, biology computing, perturbation theory, biological organs, data analysisOther keywords: gene interaction strength, cancer‐related pathways, differentially expressed genes, biological experiments, signal perturbation propagation, signalling pathway impact analysis methods, Pearson correlation coefficient, mutual information, colorectal cancer dataset analysis, pancreatic cancer dataset, PSPIA, MSPIA     

Surface wettability of plasma SiOx:H nanocoating-induced endothelial cells' migration and the associated FAK-Rho GTPases signalling pathways

Vascular endothelial cell (EC) adhesion and migration are essential processes in re-endothelialization of implanted biomaterials. There is no clear relationship and mechanism between EC adhesion and migration behaviour on surfaces with varying wettabilities. As model substrates, plasma SiO_x:H nanocoatings with well-controlled surface wettability (with water contact angles in the range of 98.5 ± 2.3° to 26.3 ± 4.0°) were used in this study to investigate the effects of surface wettability on cell adhesion/migration and associated protein expressions in FAK-Rho GTPases signalling pathways. It was found that EC adhesion/migration showed opposite behaviour on the hydrophilic and hydrophobic surfaces (i.e. hydrophobic surfaces promoted EC migration but were anti-adhesions). The number of adherent ECs showed a maximum on hydrophilic surfaces, while cells adhered to hydrophobic surfaces exhibited a tendency for cell migration. The focal adhesion kinase (FAK) inhibitor targeting the Y-397 site of FAK could significantly inhibit cell adhesion/migration, suggesting that EC adhesion and migration on surfaces with different wettabilities involve (p)FAK and its downstream signalling pathways. Western blot results suggested that the FAK-Rho GTPases signalling pathways were correlative to EC migration on hydrophobic plasma SiO_x:H surfaces, but uncertain to hydrophilic surfaces. This work demonstrated that surface wettability could induce cellular behaviours that were associated with different cellular signalling events.     

Systematic construction and prediction of the arrangement of the strands of sandwich proteins

The problem of predicting the three-dimensional structure of a protein starting from its amino acid sequence is regarded as one of the most important open problems in biology. Here, we solve aspects of this problem for the so-called sandwich proteins that constitute a large class of proteins consisting of only β-strands arranged in two sheets. A breakthrough for this class of proteins was announced in Kister et al. (Kister et al. 2002 Proc. Natl Acad. Sci. USA 99, 14 137–14 141), in which it was shown that sandwich proteins contain a certain invariant substructure called interlock. It was later noted that approximately 90% of the observed sandwich proteins are canonical, namely they are generated by certain geometrical structures. Here, employing a topological investigation, we prove that interlocks and geometrical structures are the direct consequence of certain biologically motivated fundamental principles. Furthermore, we construct all possible canonical motifs involving 6–10 strands. This construction limits dramatically the number of possible motifs. For example, for sandwich proteins with nine strands, the a priori number of possible canonical motifs exceeds 360 000, whereas our construction yields only 49 geometrical structures and 625 canonical motifs.     

Estimating Bounds on Collisional Relaxation Rates of Spin-Polarized 87Rb Atoms at Ultracold Temperatures

We present quantum scattering calculations for the collisional relaxation rate coefficient of spin-polarized ⁸⁷Rb(f = 2,m = 2) atoms, which determines the loss rate of cold Rb atoms from a magnetic trap. Unlike the lighter alkali atoms, spin-polarized ⁸⁷Rb atoms can undergo dipolar relaxation due to both the normal spin-spin dipole interaction and a second-order spin-orbit interaction with distant electronic states of the dimer. We present ab initio calculations for the second-order spin-orbit terms for both Rb₂ and Cs₂. The corrections lead to a reduction in the relaxation rate for ⁸⁷Rb. Our primary concern is to analyze the sensitivity of the ⁸⁷Rb trap loss to the uncertainties in the ground state molecular potentials. Since the scattering length for the a³Σ⁺_u state is already known, the major uncertainties are associated with the X¹Σ⁺_g potential. After testing the effect of systematically modifying the short-range form of the molecular potentials over a reasonable range, and introducing our best estimate of the second-order spin-orbit interaction, we estimate that in the low temperature limit the rate coefficient for loss of Rb atoms from the f = 2,m = 2 state is between 0.4 × 10⁻¹⁵ cm³/s and 2.4 × 10⁻¹⁵ cm³/s (where this number counts two atoms lost per collision). In a pure condensate the rate coefficient would be reduced by 1/2.     

Theoretical aspects of charge correlations in θ-(BEDT-TTF)2X

A review is given on the theoretical studies of charge correlations in θ-(BEDT-TTF)₂X. Various studies show that within a purely electronic model on the θ-type lattice with on-site U and nearest neighbor V_p and V_c interactions, the diagonal stripe, c-axis three-fold, and the vertical stripe charge correlations are favored in the regime V_p<V_c, V_p∼V_c, and V_p>V_c, respectively. In the realistic parameter regime of V_p∼V_c, there is competition between the c-axis three fold state and diagonal stripe state. Since these are different from the experimentally observed a-axis three fold and the horizontal stripe charge correlations, additional effects have to be included in order to understand the experiments. The electron–lattice coupling, which tends to distort the lattice into the θ_d-type, is found to favor the horizontal stripe state, suggesting that the occurrence of this stripe ordering in the actual materials may not be of purely electronic origin. On the other hand, distant electron–electron interactions have to be considered in order to understand the a-axis three fold correlation, whose wave vector is close to the nesting vector of the Fermi surface. These studies seem to suggest that the minimal model to understand the charge correlation in θ-(BEDT-TTF)₂X may be more complicated than expected. Future problems regarding the competition between different types of charge correlations are discussed.     

DNA double-strand break repair: a theoretical framework and its application

DNA double-strand breaks (DSBs) are formed as a result of genotoxic insults, such as exogenous ionizing radiation, and are among the most serious types of DNA damage. One of the earliest molecular responses following DSB formation is the phosphorylation of the histone H2AX, giving rise to γH2AX. Many copies of γH2AX are generated at DSBs and can be detected in vitro as foci using well-established immuno-histochemical methods. It has previously been shown that anti-γH2AX antibodies, modified by the addition of the cell-penetrating peptide TAT and a fluorescent or radionuclide label, can be used to visualize and quantify DSBs in vivo. Moreover, when labelled with a high amount of the short-range, Auger electron-emitting radioisotope, ¹¹¹In, the amount of DNA damage within a cell can be increased, leading to cell death. In this report, we develop a mathematical model that describes how molecular processes at individual sites of DNA damage give rise to quantifiable foci. Equations that describe stochastic mean behaviours at individual DSB sites are derived and parametrized using population-scale, time-series measurements from two different cancer cell lines. The model is used to examine two case studies in which the introduction of an antibody (anti-γH2AX-TAT) that targets a key component in the DSB repair pathway influences system behaviour. We investigate: (i) how the interaction between anti-γH2AX-TAT and γH2AX effects the kinetics of H2AX phosphorylation and DSB repair and (ii) model behaviour when the anti-γH2AX antibody is labelled with Auger electron-emitting ¹¹¹In and can thus instigate additional DNA damage. This work supports the conclusion that DSB kinetics are largely unaffected by the introduction of the anti-γH2AX antibody, a result that has been validated experimentally, and hence the hypothesis that the use of anti-γH2AX antibody to quantify DSBs does not violate the image tracer principle. Moreover, it provides a novel model of DNA damage accumulation in the presence of Auger electron-emitting ¹¹¹In that is supported qualitatively by the available experimental data.     

Crosstalk between pathways enhances the controllability of signalling networks

The control of complex networks is one of the most challenging problems in the fields of biology and engineering. In this study, the authors explored the controllability and control energy of several signalling networks, which consisted of many interconnected pathways, including networks with a bow‐tie architecture. On the basis of the theory of structure controllability, they revealed that biological mechanisms, such as cross‐pathway interactions, compartmentalisation and so on make the networks easier to fully control. Furthermore, using numerical simulations for two realistic examples, they demonstrated that the control energy of normal networks with crosstalk is lower than in networks without crosstalk. These results indicate that the biological networks are optimally designed to achieve their normal functions from the viewpoint of the control theory. The authors’ work provides a comprehensive understanding of the impact of network structures and properties on controllability.Inspec keywords: genetics, numerical analysis, control theoryOther keywords: signalling network controllability, interconnected pathways, bow‐tie architecture, structure controllability, biological mechanisms, cross‐pathway interactions, numerical simulations, biological networks, control theory, gene regulatory network     

Towards elucidating the connection between epithelial–mesenchymal transitions and stemness

Epithelial cells undergoing epithelial-to-mesenchymal transitions have often been shown to behave as cancer stem cells, but the precise molecular connection remains elusive. At the genetic level, stemness is governed by LIN28/let-7 double inhibition switch, whereas EMT/MET is controlled by miR-200/ZEB double inhibition circuit and LIN28 is inhibited by miR-200, coupling the two modules. Here, using a specially devised theoretical framework to investigate the dynamics of the LIN28/let-7 system, we show that it can operate as a three-way switch (between low, high and intermediate LIN28 levels termed the D, U and hybrid D/U states) similar to the three-way operation of the miR-200/ZEB circuit that allows for the existence of a hybrid epithelial/mesenchymal (E/M) phenotype. We find significant correspondence between the existence of the three states of the two circuits: E–D, M–U and E/M–D/U. Incorporating the activation of OCT4 by LIN28, we find that the hybrid E/M phenotype has high likelihood (when compared with either the E or M states) to gain stemness. Combining the LIN28/let-7 regulation by NF-κB and c-MYC, we find that NF-κB, but not c-MYC, elevates the likelihood of E/M phenotype to gain stemness. Our results are consistent with emerging concept that partial EMT can lead to stemness.     

Searching for motifs in the behaviour of larval Drosophila melanogaster and Caenorhabditis elegans reveals continuity between behavioural states

We present a novel method for the unsupervised discovery of behavioural motifs in larval Drosophila melanogaster and Caenorhabditis elegans. A motif is defined as a particular sequence of postures that recurs frequently. The animal''s changing posture is represented by an eigenshape time series, and we look for motifs in this time series. To find motifs, the eigenshape time series is segmented, and the segments clustered using spline regression. Unlike previous approaches, our method can classify sequences of unequal duration as the same motif. The behavioural motifs are used as the basis of a probabilistic behavioural annotator, the eigenshape annotator (ESA). Probabilistic annotation avoids rigid threshold values and allows classification uncertainty to be quantified. We apply eigenshape annotation to both larval Drosophila and C. elegans and produce a good match to hand annotation of behavioural states. However, we find many behavioural events cannot be unambiguously classified. By comparing the results with ESA of an artificial agent''s behaviour, we argue that the ambiguity is due to greater continuity between behavioural states than is generally assumed for these organisms.