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We consider linear stability of travelling waves in a thin-film model for two-fluid Couette flow when a thin layer of the more viscous fluid resides next to the stationary wall. We prove that in a neighbourhood of a bifurcation point, characterized by a positive integer kb , the principal branch (kb=1) is spectrally stable while all other branches (kb>1) are spectrally unstable. For larger amplitude travelling waves, we establish a number of conditional theorems where the conditions were checked with help of computer assist for a set of parameter values. Using these theorems, we rigorously confirm earlier numerical evidence (D. Papageorgiou & S. Tanveer, Proc. R. Soc. A, (doi:10.1098/rspa.2019.0367)) on stability and instability of travelling waves over a range of parameters. [ABSTRACT FROM AUTHOR]

The biosurfactant production can enhance the hydrocarbon biodegradation, as the hydrophobicity of these compounds reduces the degradation rates. Much of the attention was given to microbial hydrocarbon biodegradation, while limited work is present regarding the capacity of fungal biosurfactants for enhancing the remediation process. This research work identified the potential of biosurfactant production and hydrocarbon degradation of selected fungal strains belonging to Aspergillus, Penicillium, and Candida genera in contrast to a hydrocarbon-degrading and biosurfactant non-producing fungal strain. The highest biodegradation was noted for Aspergillus niger FA5 (90.7%), followed by Penicillium chrysogenum FP4 and Aspergillus terreus FP6 (87.4 and 85.0%, respectively), and lastly, Candida sp. FG2 (80.1%). Biosurfactant-producing hydrocarbon degrading fungal strains A. niger FA5, P. chrysogenum FP4, A. terreus FP6, and Candida sp. FG2 degraded hydrocarbons 1.32-, 1.27-, 1.24-, and 1.18-fold higher than non-producing A. flavus FP10 (68.6%). When the data were analyzed for correlation, hydrocarbon degradation was found negatively corelated to surface tension (r = –0.747, p = 0.005), while positively correlated with emulsification index (r = 0.964, p < 0.001), and cell hydrophobicity (r = 0.835, p < 0.001). The results indicate that fungi capable of attaching hydrocarbons at high concentration to the cell surface and effectively reducing surface tension were able to exhibit significant improvements in the rate of hydrocarbon degradation. Hence, it is concluded that if a fungus can produce biosurfactant that can improve hydrocarbon emulsification and reduce surface tension, the hydrocarbon breakdown can be accelerated from 12 to 22% compared to non-producers. [ABSTRACT FROM AUTHOR]

We consider instability of the flat interface in a two-layer Couette flow model developed earlier (Kalogirou & Papageorgiou, 2016, J. Fluid Mech.802, 5–36; Katsiavria & Papageorgiou, 2022, Wave Motion114, 103018. (doi:10.1016/j.wavemoti.2022.103018)) for a thin layer near one of the walls. For the case when the less viscous fluid resides next to the moving wall, we find that even a small slip effect at the interface can destabilize an otherwise highly stable flow to the Turing-type instability. The singular effect of small slip in an otherwise very stable configuration may have important ramifications in physical and technological applications. The neutral points of the dispersion relation give rise to travelling wave solutions that are continued to finite amplitude numerically and their linear stability properties identified for a set of parameter values for disturbances that include subharmonic modes with twice the wavelength of the nonlinear travelling wave. We determined Hopf and regular bifurcation points of travelling waves and rigorously justified their existence for some set of parameter values. Weakly nonlinear analysis close to bifurcation from a flat state is also presented for small amplitude waves in general. We also present global existence and regularity results for periodic initial conditions without any restriction on parameters. [ABSTRACT FROM AUTHOR]

Multiplexing approaches using tandem mass tags with a carrier proteome to boost sensitivity have advanced single cell proteomics by mass spectrometry (SCoPE-MS). Here, we probe the carrier proteome effects in single cell proteomics with mixed species TMTpro-labeled samples. We demonstrate that carrier proteomes, while increasing overall identifications, dictate which proteins are identified. We show that quantitative precision and signal intensity are limited at high carrier levels, hindering the recognition of regulated proteins. Guidelines for optimized mass spectrometry acquisition parameters and best practices for fold-change or protein copy number-based comparisons are provided. Ye et al. address a highly debated aspect of many recent single cell proteomics studies, the extent and impact of the carrier proteome. Through deployment of a mixed-species sample at various spike-in levels, they set up an experimental system for further exploration of the carrier effects on TMT-based quantification of ultra-low input samples. [ABSTRACT FROM AUTHOR]

This paper is concerned with analysis and computations of a non-local thin-film model developed in Kalogirou & Papageorgiou (J. Fluid Mech. 802, 5-36, 2016) for a perturbed two-layer Couette flow when the thickness of the more viscous fluid layer next to the stationary wall is small compared to the thickness of the less viscous fluid. Travelling wave solutions and their stability are determined numerically, and secondary bifurcation points are identified in the process. We also determine regions in parameter space where bistability is observed with two branches being linearly stable at the same time. The travelling wave solutions are mathematically justified through a quasi-solution analysis in a neighbourhood of an empirically constructed approximate solution. This relies in part on precise asymptotics of integrals of Airy functions for large wave numbers. The primary bifurcation about the trivial state is shown rigorously to be supercritical, and the dependence of bifurcation points, as a function of Reynolds number R and the primary wavelength 2πν-1/2 of the disturbance, is determined analytically. [ABSTRACT FROM AUTHOR]

We use a recently developed method [1,2] to determine approximate expression for tritronquée solution for P-1: y ″ + 6 y 2 − x = 0 in a domain D with rigorous bounds. In particular we rigorously confirm the location of the closest singularity from the origin to be at x = − 770766 323285 = − 2.3841687675 ⋯ to within 5 × 10 − 6 accuracy, in agreement with previous numerical calculations [6] . [ABSTRACT FROM AUTHOR]

This paper presents a simple and effective new numerical scheme for the computation of electrostatic fields exterior to a collection of close-to-touching discs. The method is presented in detail for the twodisc case. The key idea is to represent the required complex potential using a hybrid set of basis functions comprising the usual Fourier-Laurent expansion about each circle centre complemented by a subsidiary expansion in a variable associated with conformal mapping of the physical domain to a concentric annulus domain. We also rigorously prove that there is a representation of the solution in the hybrid basis with a faster decay rate of coefficients than is obtained by using a nonhybrid basis, thereby providing a rationalization for the success of the method. The numerical scheme is easy to implement and adaptable to the case of multiple close-to-touching cylinders. [ABSTRACT FROM AUTHOR]

Through Borel summation methods, we analyze the Boussinesq equations for coupled fluid velocity and temperature fields: (1) u t − ν Δ u = − P [ u ⋅ ∇ u − a e 2 Θ ] + f Θ t − μ Δ Θ = − u ⋅ ∇ Θ . We prove that an equivalent system of integral equations in the Borel variable p ∈ R + dual to 1 / t has a unique solution in a class of exponentially bounded functions, implying the existence of a classical solution to (1) in a complex t -region that includes a real positive time axis segment. For analytic initial data and forcing, it is shown that the solution is Borel summable, implying that formal series in powers of t is Gevrey-1 asymptotic, and within the time interval of existence, the solution remains analytic with the same analyticity strip width as the initial data and forcing. We also determine conditions on the integral equation solution that improve the estimate for existence time. [ABSTRACT FROM AUTHOR]

This paper contains details of mechanical testing of double cantilever beam composite specimens comprising a vacuum-assisted resin transfer molding–infused parent plate and a hand laid-up upper plate simulating a typical blade repair. The testing was carried out as part of an effort to optimize a new repair resin for a wind turbine blade manufacturing company. A number of commercial suppliers were contacted and nine resins with different formulations were selected for screening. Out of these, six were shortlisted for initial testing which was carried out in accordance with ASTM D 5528 (Test Method for Mode I interlaminar fracture toughness of unidirectional fiber-reinforced polymer matrix composites) using double cantilever beam specimens. The fracture toughness values obtained from testing these repair resin candidates were compared to values obtained from the repair resin currently being used and also to those of the main blade resin. The top three repair resin candidates were identified from the double cantilever beam testing. [ABSTRACT FROM PUBLISHER]

We use a recently developed method [O. Costin, M. Huang, and W. Schlag, Nonlin-earity, 25 (2012), pp. 125-164], [O. Costin, M. Huang, and S. Tanveer, Duke Math. J., 163 (2014), pp. 665-704] to find accurate analytic approximations with rigorous error bounds for the classic similarity solution of Blasius of the boundary layer equation in fluid mechanics, the two-point boundary value problem f'" + f f" = 0 with f(0) = f'(0) = 0 and limx→∞ f'(x) = 1. The approximation is given in terms of a polynomial in [0,5/2] and in terms of the error function in [5/2, ∞). The two representations for the solution in different domains match at x = 5/2 determining all free parameters in the problem, in particular f"(0) = 0.469600 ± 0.000022 at the wall. The method can in principle provide approximations to any desired accuracy for this or wide classes of linear or nonlinear differential equations with initial or boundary value conditions. The analysis relies on controlling the errors in the approximation through contraction mapping arguments, using energy bounds for the Green's function of the linearized problem. [ABSTRACT FROM AUTHOR]

Transformation of engineered Escherichia coli into a robust microbial factory is contingent on precise control of metabolism. Yet, the throughput of omics technologies used to characterize cell components has lagged far behind our ability to engineer novel strains. To expand the utility of quantitative proteomics for metabolic engineering, we validated and optimized targeted proteomics methods for over 400 proteins from more than 20 major pathways in E. coli metabolism. Complementing these methods, we constructed a series of synthetic genes to produce concatenated peptides (QconCAT) for absolute quantification of the proteins and made them available through the Addgene plasmid repository ( www.addgene.org ). To facilitate high sample throughput, we developed a fast, analytical-flow chromatography method using a 5.5-min gradient (10 min total run time). Overall this toolkit provides an invaluable resource for metabolic engineering by increasing sample throughput, minimizing development time and providing peptide standards for absolute quantification of E. coli proteins. [ABSTRACT FROM AUTHOR]

General perturbations of a spherical gas bubble in a compressible and inviscid fluid with surface tension were proved in [A, M. Shapiro and M. I. Weinstein, SIAM J. Math. Anal., 43 (2011), pp. 828-876], in the linearized approximation, to decay exponentially, ∼ e-Γt, Γ > 0, as time advances. Formal asymptotic and numerical evidence led to the conjecture that Γ ≈ A/ε We/ε² exp(-BWe/ε²), where 0 < ε ≪ 1 is the Mach number and A and B are positive constants. In this paper, we prove this conjecture and calculate A and B to leading order in ε. [ABSTRACT FROM AUTHOR]

Using a vortex sheet method we prove global existence of a near-circular initial bubble in a Hele-Shaw cell with surface tension and a generally finite nonzero viscosity ratio between fluids inside and outside the bubble. The circular shape is shown to be asymptotically stable for all sufficiently smooth small perturbations. The initial condition in this case, while smooth, need not be analytic. [ABSTRACT FROM PUBLISHER]

Abstract: Successful metabolic engineering relies on methodologies that aid assembly and optimization of novel pathways in microbes. Many different factors may contribute to pathway performance, and problems due to mRNA abundance, protein abundance, or enzymatic activity may not be evident by monitoring product titers. To this end, synthetic biologists and metabolic engineers utilize a variety of analytical methods to identify the parts of the pathway that limit production. In this study, targeted proteomics, via selected-reaction monitoring (SRM) mass spectrometry, was used to measure protein levels in Escherichia coli strains engineered to produce the sesquiterpene, amorpha-4,11-diene. From this analysis, two mevalonate pathway proteins, mevalonate kinase (MK) and phosphomevalonate kinase (PMK) from Saccharomyces cerevisiae, were identified as potential bottlenecks. Codon-optimization of the genes encoding MK and PMK and expression from a stronger promoter led to significantly improved MK and PMK protein levels and over three-fold improved final amorpha-4,11-diene titer (>500mg/L). [Copyright &y& Elsevier]

We consider the Navier-Stokes initial value problem, [image omitted] where P is the Hodge-Projection to divergence free vector fields in the assumption that |f|μ, β < ∞ and | v0 |μ+2, β < ∞ for β ≥ 0,μ > 3, where [image omitted] and fˆ (k) = F [f (·)] (k) is the Fourier transform in x. By Borel summation methods we show that there exists a classical solution in the form [image omitted] t ∈ , [image omitted], and we estimate α in terms of | vˆ0 |μ+2, β and | fˆ |μ, β. We show that | vˆ (·; t) |μ+2, β < ∞. Existence and t-analyticity results are analogous to Sobolev spaces ones. An important feature of the present approach is that continuation of v beyond t = α-1 becomes a growth rate question of U(·, p) as p → ∞, U being is a known function. For now, our estimate is likely suboptimal. A second result is that we show Borel summability of v for v0 and f analytic. In particular, Borel summability implies a the Gevrey-1 asymptotics result: [image omitted], where [image omitted], with A0 and B0 are given in terms of to v0 and f and for small t, with [image omitted], [image omitted] [ABSTRACT FROM AUTHOR]

Abstract: An interfacial approximation of the streamer stage in the evolution of sparks and lightning can be written as a Laplacian growth model regularized by a ‘kinetic undercooling’ boundary condition. We study the linear stability of uniformly translating circles that solve the problem in two dimensions. In a space of smooth perturbations of the circular shape, the stability operator is found to have a pure point spectrum. Except for the eigenvalue for infinitesimal translations, all eigenvalues are shown to have negative real part. Therefore perturbations decay exponentially in time. We calculate the spectrum through a combination of asymptotic and series evaluation. In the limit of vanishing regularization parameter, all eigenvalues are found to approach zero in a singular fashion, and this asymptotic behavior is worked out in detail. A consideration of the eigenfunctions indicates that a strong intermediate growth may occur for generic initial perturbations. Both the linear and the nonlinear initial value problem are considered in a second paper. [Copyright &y& Elsevier]

Abstract: We consider a system of n-th order nonlinear quasilinear partial differential equations of the form with , for and large in a poly-sector S in ( and ). The principal part of the constant coefficient n-th order differential operator is subject to a cone condition. The nonlinearity g and the functions and u satisfy analyticity and decay assumptions in S. The paper shows existence and uniqueness of the solution of this problem and finds its asymptotic behavior for large . Under further regularity conditions on g and which ensure the existence of a formal asymptotic series solution for large to the problem, we prove its Borel summability to the actual solution u. The structure of the nonlinearity and the complex plane setting preclude standard methods. We use a new approach, based on Borel–Laplace regularization and Écalle acceleration techniques to control the equation. These results are instrumental in constructive analysis of singularity formation in nonlinear PDEs with prescribed initial data, an application referred to in the paper. In special cases motivated by applications we show how the method can be adapted to obtain short-time existence, uniqueness and asymptotic behavior for small t, of sectorially analytic solutions, without size restriction on the space variable. [Copyright &y& Elsevier]

We introduce a method of rigorous analysis of complex singularities for nonlinear higher order partial differential equations (PDEs) with prescribed initial data. The method is applied to determine rigorously the asymptotic structure of singularities of the modified Harry–Dym equation for small time at the boundaries of the sector of analyticity. Previous work (Costin and Tanveer, 2000; submitted) shows existence, uniqueness, and Borel summability of solutions of general PDEs. It is shown that the solution to the above initial value problem is represented convergently by a series in a fractional power of t down to a small annular neighborhood of a singularity of the leading order equation. We deduce that the exact solution has a singularity nearby having, to leading order, the same type. [ABSTRACT FROM AUTHOR]

The influence of convection caused by horizontal heat transfer through the sides of a vertical Bridgman apparatus is studied analytically. The case when the heat transfer across the side walls is small is considered, so that the resulting interfacial deformation and fluid velocities are also small. This allows one to linearize the Navier-Stokes equations and express the interfacial conditions about a planar interface through a Taylor expansion. Using a no-tangential stress condition on the side walls, asymptotic expressions for both the interfacial slope and radial segregation at the crystal-melt interface are obtained in closed form in the limit of large thermal Rayleigh number. It is suggested that these can be reduced by appropriately controlling a specific heat transfer property at the edge of the insulation zone on the solid side. [ABSTRACT FROM AUTHOR]

Equations governing the motion of a specific class of singularities of the Euler equation in the extended complex spatial domain are derived. Under some assumptions, it is shown how this motion is dictated by the smooth part of the complex velocity at a singular point in the unphysical domain. These results are used to relate the motion of complex singularities to the stability of steady solutions of the Euler equation. A sufficient condition for instability is conjectured. Several examples are presented to demonstrate the efficacy of this sufficient condition which include the class of elliptical flows and the Kelvin–Stuart cat’s eye. [ABSTRACT FROM AUTHOR]

Exact solutions are presented for a steady stream of bubbles in a Hele–Shaw cell when the effect of surface tension is neglected. These solutions form a three-parameter family. For specified area and distance between bubbles, the speed of the bubble remains arbitrary when surface tension is neglected. However, numerical and analytical evidence indicates that this arbitrariness is removed by the effect of surface tension. The branch of solutions that corresponds to the McLean–Saffman finger solution were primarily studied. A dramatic increase was observed in bubble speeds when the distance between bubbles is on the order of a bubble diameter, which may have relevance to experiments done by Maxworthy [J. Fluid Mech. 173, 95 (1986)]. [ABSTRACT FROM AUTHOR]

The effect of the thin film between a bubble of a less viscous fluid and the transverse walls on the velocity of steady propagation of the bubble is explored. The estimates suggest that the film corrections for small capillary number cannot account for the large discrepancy between the experimentally observed [Phys. Fluids 31, 18 (1988)] bubble velocities and the theoretical values based on a simplified theory. However, if the thin film is ignored and it is assumed that the contact angle between the interface and the plate varies at different points of the interface in some prescribed manner, then it is possible to account in a qualitative way for the small bubble velocities in the Kopf-Sill--Homsy experiment. [ABSTRACT FROM AUTHOR]

Presents a theory of exact solutions for the quasi-steady evolution of a plane annular viscous blob of fluid driven by surface tension. Existence of an infinite number of conserved quantities associated with the flow for a certain general class of initial conditions; Similarities between the free boundary problems in simply connected domains for Hele-Shaw flow and Stokes flow with nonzero surface tension.

Presents a general theory of exact solutions for a simply connected, plane, slow viscous fluid blob with surface tension. Existence of an infinite number of conserved quantities associated with the exact solutions; Mathematical formulation; Conformal mapping representation.

The linear stability of a steadily moving bubble or a finger in a Hele-Shaw cell is considered in the case when gravity and the ratio between the viscosities of the less and more viscous fluids are nonzero. The effect of gravity is easily incorporated by a transformation of parameters introduced previously by Saffman and Taylor [Proc. R. Soc. London Ser. A 245, 312 (1958)] for the steady flow, which makes the time-dependent flows with and without gravity equivalent. For the nonzero viscosity ratio, the transformation of parameters introduced by Saffman and Taylor also makes steady finger and bubble flows with nonzero and zero viscosity ratios equivalent. However, for the unsteady ease, there is no such equivalence and so a complete calculation is carried out to investigate the effect of the nonzero viscosity ratio on the stability of fingers and bubbles. The incorporation of the finite viscosity ratio is found not to qualitatively alter the linear stability features obtained in earlier work for the zero viscosity ratio, although there are quantitative differences in the growth or decay rate of various modes. For any surface tension, numerical calculation suggests that the McLean-Saffman branch of bubbles [Phys. Fluids 30, 651 (1987)] of arbitrary size is stable, whereas all the other branches are unstable. For a small bubble that is circular, the eigenvalues of the stability operator are found explicitly. The previous analytic theory for the stability of the finger in the limit of zero surface tension is extended to include the ease of the finite viscosity ratio. It is found that, as in the case of bubbles, the finite viscosity ratio does not alter qualitatively any of the features obtained previously for the zero viscosity ratio. [ABSTRACT FROM AUTHOR]

The linear stability of steadily moving bubbles in a Hele–Shaw cell is investigated. It is shown analytically that without the effect of surface tension, the bubbles are linearly unstable with the stability operator having a continuous spectrum. For small bubbles that are circular, analytical calculations also show that any amount of surface tension stabilizes a bubble. Numerical calculations suggest that the branch of bubble solutions that, in the limit of large area, corresponds to the McLean–Saffman finger is stable for any nonzero surface tension. However, the decay rate of disturbances on the McLean–Saffman branch depends appreciably on the bubble size even for large bubbles. This suggests that the stability results on this branch cannot be immediately extrapolated to the McLean–Saffman fingers. For another branch of bubble solution, which in the limit or large area corresponds to the first of the Romero–Vanden-Broeck finger solutions, numerical evidence suggests that it is unstable to one symmetric and one antisymmetric mode for any surface tension. The symmetric unstable mode tends to break the tip of the bubble and the growth rate of this mode is unaffected by further increase in bubble size, once the bubble is large enough. This suggests that there is an analogous instability for the finger, and this agrees with the numerical findings of Kessler and Levine [Phys. Rev. A 33, 2632 (1986)]. Agreement is noted in the quantitative comparison of the growth rate with the predictions [Tanveer, Phys. Fluids 30, xxxx (1987)] on the limiting growth rate for the symmetric unstable mode for the first Romero–Vanden-Broeck branch of finger solution. [ABSTRACT FROM AUTHOR]

An analytic theory is presented for the linear stability of the Saffman–Taylor finger in a Hele–Shaw cell. Eigenvalues of the stability operator are determined in the limit of zero surface tension and it is found that all modes for the McLean–Saffman branch of solutions [J. Fluid Mech. 102, 455 (1980)] are neutrally stable, whereas other branches first calculated by Romero (Ph.D. thesis, California Institute of Technology, 1982) and Vanden-Broeck [Phys. Fluids 26, 2033 (1983)] are unstable to arbitrary infinitesimal disturbances. It is also shown that the Saffman–Taylor discrete set of eigenvalues is a special case of a continuous unstable spectrum for zero surface tension. The introduction of any amount of surface tension perturbs the corresponding eigenmodes such that the finger boundary is a nonanalytic curve in general. Only transcendentally small terms in surface tension are responsible for the nonanalyticity of the finger boundary as in the case of Saffman–Taylor steady finger solutions of arbitrary finger width. [ABSTRACT FROM AUTHOR]

An analytic theory is presented for the selection mechanism of a symmetric finger with a discrete set of possible width from a continuum of nonsymmetric Saffman–Taylor finger solutions of arbitrary width. Both linear and nonlinear analyses have been carried out and in almost all cases, it is shown analytically that nonsymmetric solutions do not exist for nonzero surface tension if the finger boundary is assumed to be smooth. In the other cases, numerical calculations appear to support the same conclusions. In the asymptotic range, the predicted set of countably infinite possible finger widths according to nonlinear analysis agree with the previous analytical results of Combescot et al. [Phys. Rev. Lett. 56, 2036 (1986)] for a finger assumed to be symmetric about the channel centerline. The predicted coefficient of the power law dependence of finger width on surface tension for the first few of these solutions, i.e., on the branches first calculated by Mclean–Saffman [J. Fluid Mech. 102, 455 (1980)], Romero (Ph.D. thesis, California Institute of Technology, 1982) and Vanden-Broeck [Phys. Fluids 26, 2033 (1983)], are in agreement with Tanveer’s [Phys. Fluids 30, 651 (1987)] estimate of this coefficient based on numerical calculations of bubbles. It is also shown that the nonlinear analysis has the same qualitative features as the linear analysis and, in the asymptotic range, the agreement is close. [ABSTRACT FROM AUTHOR]

Exact solutions are presented for steadily moving bubbles in a Hele-Shaw cell when the effect of surface tension is neglected. These solutions form a three-parameter family. For specified area, both the speed of the bubble and the distance of its centroid from the channel centerline remain arbitrary when surface tension is ignored. However, numerical evidence suggests that this twofold arbitrariness is removed by the effect of surface tension, i.e., for given bubble area and surface tension, solutions exist only when the bubble velocity and the centroid distance from the channel centerline attain one or more isolated values. From a limited numerical search, no nonsymmetric solutions could be found; however, a branch of symmetric bubble solutions that was not found in earlier work was found. This branch corresponds to one of the Romero-Vanden-Broeck branch of finger solutions when the bubble size is large. A new procedure for numerical calculations of bubble solutions in the presence of surface tension is presented and is found to work very well for reasonably large bubbles, unlike the previous method of Tanveer [Phys. Fluids 29, 3537 (1986)]. The precise power law dependence of bubble velocity on surface, tension for small surface tension is explored for bubbles of different area. Agreement is noted with recent analytical results for a finger. [ABSTRACT FROM AUTHOR]

SOCS2 is a pleiotropic E3 ligase. Its deficiency is associated with gigantism and organismal lethality upon inflammatory challenge. However, mechanistic understanding of SOCS2 function is dismal due to our unawareness of its protein substrates. We performed a mass spectrometry based proteomic profiling upon SOCS2 depletion and yield quantitative data for ~4200 proteins. Through this screen we identify a novel target of SOCS2, the serine-threonine kinase NDR1. Over-expression of SOCS2 accelerates turnover, while its knockdown stabilizes, endogenous NDR1 protein. SOCS2 interacts with NDR1 and promotes its degradation through K48-linked ubiquitination. Functionally, over-expression of SOCS2 antagonizes NDR1-induced TNFα-stimulated NF-κB activity. Conversely, depletion of NDR1 rescues the effect of SOCS2-deficiency on TNFα-induced NF-κB transactivation. Using a SOCS2−/− mice model of colitis we show that SOCS2-deficiency is pro-inflammatory and negatively correlates with NDR1 and nuclear p65 levels. Lastly, we provide evidence to suggest that NDR1 acts as an oncogene in prostate cancer. To the best of our knowledge, this is the first report of an identified E3 ligase for NDR1. These results might explain how SOCS2-deficiency leads to hyper-activation of NF-κB and downstream pathological implications and posits that SOCS2 induced degradation of NDR1 may act as a switch in restricting TNFα-NF-κB pathway. [ABSTRACT FROM AUTHOR]

Cancer risk after ionizing radiation (IR) is assumed to be linear with the dose; however, for low doses, definite evidence is lacking. Here, using temporal multi-omic systems analyses after a low (LD; 0.1 Gy) or a high (HD; 1 Gy) dose of X-rays, we show that, although the DNA damage response (DDR) displayed dose proportionality, many other molecular and cellular responses did not. Phosphoproteomics uncovered a novel mode of phospho-signaling via S12-PPP1R7, and large-scale dephosphorylation events that regulate mitotic exit control in undamaged cells and the G2/M checkpoint upon IR in a dose-dependent manner. The phosphoproteomics of irradiated DNA double-strand breaks (DSBs) repair-deficient cells unveiled extended phospho-signaling duration in either a dose-dependent (DDR signaling) or independent (mTOR-ERK-MAPK signaling) manner without affecting signal magnitude. Nascent transcriptomics revealed the transcriptional activation of genes involved in NRF2-regulated antioxidant defense, redox-sensitive ERK-MAPK signaling, glycolysis and mitochondrial function after LD, suggesting a prominent role for reactive oxygen species (ROS) in molecular and cellular responses to LD exposure, whereas DDR genes were prominently activated after HD. However, how and to what extent the observed dose-dependent differences in molecular and cellular responses may impact cancer development remain unclear, as the induction of chromosomal damage was found to be dose-proportional (10–200 mGy). [ABSTRACT FROM AUTHOR]

Abstract: A balanced heterologous biosynthetic pathway in microbes is necessary to ensure high titers of the desired product. Expression of synthetic heterologous metabolic pathways in a host may not be favorable due to the toxicity of non-native metabolic intermediates and the burden of expression of genes in the pathway. Thus, optimization of gene expression is required to prevent accumulation of the toxic metabolites and to minimize burden. In this study, we used the BglBrick standard cloning vectors to optimize expression of genes in a heterologous mevalonate-based isoprenoid biosynthetic pathway and examined their impact on production of amorpha-4,11-diene, an intermediate in the biosynthesis of the antimalarial drug artemisinin. Amorpha-4,11-diene titer increased almost three-fold when HMG-CoA reductase and phosphomevalonate kinase were overexpressed relative to the original engineered pathway. In addition, selected-reaction monitoring (SRM) mass spectrometry-based targeted proteomics showed that overexpression of HMG-CoA reductase and phosphomevalonate kinase significantly enhances the titer of amorpha-4,11-diene, and that further increases in titer could be achieved if mevalonate kinase were engineered as well. [Copyright &y& Elsevier]

Abstract: Limonene is a valuable monoterpene used in the production of several commodity chemicals and medicinal compounds. Among them, perillyl alcohol (POH) is a promising anti-cancer agent that can be produced by hydroxylation of limonene. We engineered E. coli with a heterologous mevalonate pathway and limonene synthase for production of limonene followed by coupling with a cytochrome P450, which specifically hydroxylates limonene to produce POH. A strain containing all mevalonate pathway genes in a single plasmid produced limonene at titers over 400mg/L from glucose, substantially higher than has been achieved in the past. Incorporation of a cytochrome P450 to hydroxylate limonene yielded approximately 100mg/L of POH. Further metabolic engineering of the pathway and in situ product recovery using anion exchange resins would make this engineered E. coli a potential production platform for any valuable limonene derivative. [Copyright &y& Elsevier]

Abstract: Membrane potential and membrane conductance measurements have been carried out using Dowex-50Kynar membrane, sodium chloride and urea as a hydrotrope, mixture of varying composition to examine the hydrotrope effect on electrochemical character of the membrane. A significant change on membrane electrochemical character is observed in the presence of hydrotrope due to changed co-ion exclusion. The Donnan equilibrium has been incorporated to estimate the activity coefficient of counter ion, yp m, and solute, y± m in the membrane phase along with the parameter, so called Ф expressing non-ideality. Solute rejection performance of the membrane is examined when electrolyte concentration remains constant and hydrotrope concentration varies and vice-versa. In both cases, membrane specific conductance depends on NaCl and hydrotrope concentrations differently. Friction caused through the membrane by the variation in concentration of hydrotrope is greater than friction caused by the variation in concentration of NaCl. Zeta potential is sensitive to the variation of hydrotrope concentration but insensitive to the variation of electrolyte concentration. The membrane system shows the behavior of NF membrane because Pe≪1 is estimated in both cases. [Copyright &y& Elsevier]

Abstract: Fatty acids are important precursors to biofuels. The Escherichia coli FadR is a transcription factor that regulates several processes in fatty acid biosynthesis, degradation, and membrane transport. By tuning the expression of FadR in an engineered E. coli host, we were able to increase fatty acid titer by 7.5-fold over our previously engineered fatty acid-producing strain, reaching 5.2±0.5g/L and 73% of the theoretical yield. The mechanism by which FadR enhanced fatty acid yield was studied by whole-genome transcriptional analysis (microarray) and targeted proteomics. Overexpression of FadR led to transcriptional changes for many genes, including genes involved in fatty acid pathways. The biggest transcriptional changes in fatty acid pathway genes included fabB, fabF, and accA. Overexpression of any of these genes alone did not result in a high yield comparable to fadR expression, indicating that FadR enhanced fatty acid production globally by tuning the expression levels of many genes to optimal levels. [Copyright &y& Elsevier]

Escherichia coli has the potential to be a powerful biocatalyst for the conversion of lignocellulosic biomass into useful materials such as biofuels and polymers. One important challenge in using E. coli for the transformation of biomass sugars is diauxie, or sequential utilization of different types of sugars. We demonstrate that, by increasing the intracellular levels of the transcription factor Xy1R, the preferential consumption of arabinose before xylose can be eliminated. In addition, Xy1R augmentation must be finely tuned for robust coutilization of these two hemicellulosic sugars. Using a novel technique for scarless gene insertion, an additional copy of xylR was inserted into the araBAD operon. The resulting strain was superior at cometabolizing mixtures of arabinose and xylose and was able to produce at least 36% more ethanol than wild-type strains. This strain is a useful starting point for the development of an E. coli biocatalyst that can simultaneously convert all biomass sugars. [ABSTRACT FROM AUTHOR]

Steady, inviscid, incompressible, two-dimensional flows with vortex patches bounded by vortex sheets (Batchelor flows) are calculated numerically. Two particular cases are considered: the vortex on a plane wall (Sadovskii vortex) and the vortex in a right-angled corner. Nonlinear integral equations are derived for the shape of the bounding vortex sheet which are solved numerically. Two different formulations are employed to check the results. Previous results by Sadovskii [Appl. Math. Mech. 35, 773 (1971)] and Chernyshenko (Royal Aircraft Establishment library translations Report No. 2133, 1983) for specific values of the parameters are confirmed. Only symmetrical solutions are found to exist. [ABSTRACT FROM AUTHOR]

Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class Agaricomycetes, associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, is AA9B, a naturally occurring protein from Lentinus similis. The LsAA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of LsAA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass. [ABSTRACT FROM AUTHOR]

Longitudinal studies consistently report adverse long-term outcomes of childhood maltreatment. Little is known about the impact of childhood maltreatment on mental health among a marginalized population (New Zealand Māori); therefore, we cannot assume the effects of maltreatment are the same across the population. Associations were examined between childhood sexual abuse (CSA), childhood physical punishment (CPP) and childhood neglect (CN) (<16 years) and mental health outcomes 18–40 years, by ethnicity (Māori/non-Māori). Data from the Christchurch Health and Development Study, a study of a birth cohort of 1265 children born in Christchurch in 1977. By age 40, 17.8 % (n = 191) reported New Zealand Māori ethnic identity; 82.2 % (n = 883) were non-Māori. CSA, CPP (<16 years) were measured at 18, 21 years; CN was measured at 40 years. Major depression, anxiety disorder, suicidal ideation, alcohol abuse/dependence and cannabis abuse/dependence were measured at ages 21, 25, 30, 35 and 40 years. Childhood confounding variables controlled. Analyses were extended to include Māori ethnicity. After statistical adjustment, experience of severe childhood maltreatment increased odds of mental health problems 1.8–2.6×, compared to no maltreatment; the effects of maltreatment were similar for males and females. For Māori, some higher rates of mental health problems were seen among those maltreated, no statistically significant associations were detected after Bonferroni correction (among severe maltreatment vs. no maltreatment). Limitations should be considered when interpreting results. Exposure to childhood maltreatment has long-term effects into middle-age. Further research employing culturally-sensitive approaches may help clarify Māori childhood maltreatment outcomes. • Childhood maltreatment increases the risk of mental health problems in adulthood. • Few studies examine the long-term impact of maltreatment on New Zealand Māori. • [Study] data was gathered for this research. • Severely maltreated full sample had up to 2.6× the odds of mental health problems. • Severely, maltreated Māori did not show higher risk of mental health problems. [ABSTRACT FROM AUTHOR]

Using the simple case of the Blasius similarity solution, we illustrate a recently developed general method (Costin et al 2012 Nonlinearity25 125–64; Costin et al 2012 arXiv:1209.1009) that reduces a strongly nonlinear problem into a weakly nonlinear analysis. The basic idea is to find a quasi-solution that satisfies the nonlinear problem and boundary conditions to within small errors. Then, by decomposing the true solution , a weakly nonlinear analysis of E, using the contraction mapping theorem in a suitable space of functions provides the existence of the solution as well as bounds on the error E. The quasi-solution construction relies on a combination of exponential asymptotics and standard orthogonal polynomial representations in a finite domain. [ABSTRACT FROM AUTHOR]

The ability to solubilize lignocellulose makes certain ionic liquids (ILs) very effective reagents for pretreating biomass prior to its saccharification for biofuel fermentation. However, residual IL in the aqueous sugar solution can inhibit the growth and function of biofuel-producing microorganisms. In E. coli this toxicity can be partially overcome by the heterologous expression of an IL efflux pump encoded by eilA from Enterobacter lignolyticus. In the present work, we used microarray analysis to identify native E. coli IL-inducible promoters and develop control systems for regulating eilA gene expression. Three candidate promoters, PmarR’, PydfO’, and PydfA’, were selected and compared to the IPTG-inducible PlacUV5 system for controlling expression of eilA. The PydfA’ and PmarR’ based systems are as effective as PlacUV5 in their ability to rescue E. coli from typically toxic levels of IL, thereby eliminating the need to use an IPTG-based system for such tolerance engineering. We present a mechanistic model indicating that inducible control systems reduce target gene expression when IL levels are low. Selected-reaction monitoring mass spectrometry analysis revealed that at high IL concentrations EilA protein levels were significantly elevated under the control of PydfA’ and PmarR’ in comparison to the other promoters. Further, in a pooled culture competition designed to determine fitness, the strain containing pPmarR’-eilA outcompeted strains with other promoter constructs, most significantly at IL concentrations above 150 mM. These results indicate that native promoters such as PmarR’ can provide effective systems for regulating the expression of heterologous genes in host engineering and simplify the development of industrially useful strains. [ABSTRACT FROM AUTHOR]

Heterologous pathways used in metabolic engineering may produce intermediates toxic to the cell. Dynamic control of pathway enzymes could prevent the accumulation of these metabolites, but such a strategy requires sensors, which are largely unknown, that can detect and respond to the metabolite. Here we applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product. We apply this approach to regulate farnesyl pyrophosphate (FPP) production in the isoprenoid biosynthetic pathway in Escherichia coli. This strategy improved production of amorphadiene, the final product, by twofold over that from inducible or constitutive promoters, eliminated the need for expensive inducers, reduced acetate accumulation and improved growth. We extended this approach to another toxic intermediate to demonstrate the broad utility of identifying novel sensor-regulator systems for dynamic regulation. [ABSTRACT FROM AUTHOR]

Corneal infection with Pseudomonas aeruginosa leads to a severe immunoinflammatory lesion, often causing vision impairment and blindness. Although past studies have indicated a critical role for CD4+ T cells, particularly Th1 cells, in corneal immunopathology, the relative contribution of recently discovered Th17 and regulatory T cells is undefined. In this study, we demonstrate that after corneal P. aeruginosa infection, both Th1 and Th17 cells infiltrate the cornea with increased representation of Th17 cells. In addition to Th1 and Th17 cells, regulatory T cells also migrate into the cornea during early as well as late stages of corneal pathology. Moreover, using galectin-1 (Gal-1), an immunomodulatory carbohydrate-binding molecule, we investigated whether shifting the balance among various CD4+ T cell subsets can modulate P. aeruginosa-induced corneal immunopathology. We demonstrate in this study that local recombinant Gal-1 (rGal-1) treatment by subconjunctival injections significantly diminishes P. aeruginosa-mediated corneal inflammation through multiple mechanisms. Specifically, in our study, rGal-1 treatment significantly diminished corneal infiltration of total CD45+ T cells, neutrophils, and CD4+ T cells. Furthermore, rGal-1 treatment significantly reduced proinflammatory Th17 cell response in the cornea as well as local draining lymph nodes. Also, rGal-1 therapy promoted anti-inflammatory Th2 and IL-10 response in secondary lymphoid organs. Collectively, our results indicate that corneal P. aeruginosa infection induces a strong Th17-mediated corneal pathology, and treatment with endogenously derived protein such as Gal-1 may be of therapeutic value for the management of bacterial keratitis, a prevalent cause of vision loss and blindness in humans worldwide. [ABSTRACT FROM AUTHOR]

The plant Golgi plays a pivotal role in the biosynthesis of cell wall matrix polysaccharides, protein glycosylation, and vesicle trafficking. Golgi-localized proteins have become prospective targets for reengineering cell wall biosynthetic pathways for the efficient production of biofuels from plant cell walls. However, proteomic characterization of the Golgi has so far been limited, owing to the technical challenges inherent in Golgi purification. In this study, a combination of density centrifugation and surface charge separation techniques have allowed the reproducible isolation of Golgi membranes from Arabidopsis (Arabidopsis thaliana) at sufficiently high purity levels for in-depth proteomic analysis. Quantitative proteomic analysis, immunoblotting, enzyme activity assays, and electron microscopy all confirm high purity levels. A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. The localization of 13 newly assigned proteins to the Golgi using transient fluorescent markers further validated the proteome. A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome, marking an appreciable advancement in numbers of Golgi-localized proteins. A significant proportion of proteins likely involved in matrix polysaccharide biosynthesis were identified. The potential within this proteome for advances in understanding Golgi processes has been demonstrated by the identification and functional characterization of the first plant Golgi-resident nucleoside diphosphatase, using a yeast complementation assay. Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized. [ABSTRACT FROM AUTHOR]

Efficient biosynthesis of l-tyrosine from glucose is necessary to make biological production economically viable. To this end, we designed and constructed a modular biosynthetic pathway for l-tyrosine production in E. coli MG1655 by encoding the enzymes for converting erythrose-4-phosphate (E4P) and phosphoenolpyruvate (PEP) to l-tyrosine on two plasmids. Rational engineering to improve l-tyrosine production and to identify pathway bottlenecks was directed by targeted proteomics and metabolite profiling. The bottlenecks in the pathway were relieved by modifications in plasmid copy numbers, promoter strength, gene codon usage, and the placement of genes in operons. One major bottleneck was due to the bifunctional activities of quinate/shikimate dehydrogenase (YdiB), which caused accumulation of the intermediates dehydroquinate (DHQ) and dehydroshikimate (DHS) and the side product quinate; this bottleneck was relieved by replacing YdiB with its paralog AroE, resulting in the production of over 700 mg/liter of shikimate. Another bottleneck in shikimate production, due to low expression of the dehydroquinate synthase (AroB), was alleviated by optimizing the first 15 codons of the gene. Shikimate conversion to l-tyrosine was improved by replacing the shikimate kinase AroK with its isozyme, AroL, which effectively consumed all intermediates formed in the first half of the pathway. Guided by the protein and metabolite measurements, the best producer, consisting of two medium-copy-number, dual-operon plasmids, was optimized to produce >2 g/liter l-tyrosine at 80% of the theoretical yield. This work demonstrates the utility of targeted proteomics and metabolite profiling in pathway construction and optimization, which should be applicable to other metabolic pathways. [ABSTRACT FROM AUTHOR]

Abstract: Expression of foreign pathways often results in suboptimal performance due to unintended factors such as introduction of toxic metabolites, cofactor imbalances or poor expression of pathway components. In this study we report a 120% improvement in the production of the isoprenoid-derived sesquiterpene, amorphadiene, produced by an engineered strain of Escherichia coli developed to express the native seven-gene mevalonate pathway from Saccharomyces cerevisiae (). This substantial improvement was made by varying only a single component of the pathway (HMG-CoA reductase) and subsequent host optimization to improve cofactor availability. We characterized and tested five variant HMG-CoA reductases obtained from publicly available genome databases with differing kinetic properties and cofactor requirements. The results of our in vitro and in vivo analyses of these enzymes implicate substrate inhibition of mevalonate kinase as an important factor in optimization of the engineered mevalonate pathway. Consequently, the NADH-dependent HMG-CoA reductase from Delftia acidovorans, which appeared to have the optimal kinetic parameters to balance HMG-CoA levels below the cellular toxicity threshold of E. coli and those of mevalonate below inhibitory concentrations for mevalonate kinase, was identified as the best producer for amorphadiene (54% improvement over the native pathway enzyme, resulting in 2.5mM or 520mg/L of amorphadiene after 48h). We further enhanced performance of the strain bearing the D. acidovorans HMG-CoA reductase by increasing the intracellular levels of its preferred cofactor (NADH) using a NAD+-dependent formate dehydrogenase from Candida boidinii, along with formate supplementation. This resulted in an overall improvement of the system by 120% resulting in 3.5mM or 700mg/L amorphadiene after 48h of fermentation. This comprehensive study incorporated analysis of several key parameters for metabolic design such as in vitro and in vivo kinetic performance of variant enzymes, intracellular levels of protein expression, in-pathway substrate inhibition and cofactor management to enable the observed improvements. These metrics may be applied to a broad range of heterologous pathways for improving the production of biologically derived compounds. [Copyright &y& Elsevier]

Protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction. [ABSTRACT FROM AUTHOR]

Abstract: An interfacial approximation of the streamer stage in the evolution of sparks and lightning can be formulated as a Laplacian growth model regularized by a ‘kinetic undercooling’ boundary condition. Using this model we study both the linearized and the full nonlinear evolution of small perturbations of a uniformly translating circle. Within the linear approximation analytical and numerical results show that perturbations are advected to the back of the circle, where they decay. An initially analytic interface stays analytic for all finite times, but singularities from outside the physical region approach the interface for , which results in some anomalous relaxation at the back of the circle. For the nonlinear evolution numerical results indicate that the circle is the asymptotic attractor for small perturbations, but larger perturbations may lead to branching. We also present results for more general initial shapes, which demonstrate that regularization by kinetic undercooling cannot guarantee smooth interfaces globally in time. [Copyright &y& Elsevier]

The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of ~5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7- Å resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-A resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Ca backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed ~95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TriC's cellular substrate specificity. [ABSTRACT FROM AUTHOR]