Characterization of AMPylation on Threonine,Serine, and Tyrosine Using Mass Spectrometry

Recent studies have suggested that adenosine 5'-monophosphate (AMP) post-translational modification of proteins could represent a novel molecular signaling pathway. Mass spectrometric fragmentation characteristics of this modification have not previously been described and studied systematically. In this work, we therefore examined the fragmentation pattern of chemically synthesized peptides containing AMPylated Thr, Ser, and Tyr. The formation of characteristic ions and the influence of collision energy (CE) on the detection of characteristic ions and their relative peak intensity are reported. When peptide with AMPylated Ser/Thr underwent collision induced dissociation (CID), peaks at m/z 348.1, 136.1, and 250.1, fragments with AMP group attached, and fragments consistent with neutral loss of 347 Da were major characteristic ions; fragments consistent with neutral loss of 135 Da or 249 Da were weaker and not always detectable. The observations for Tyr AMPylation followed the same general patterns as those for Ser/Thr modification, with the exception that the ions detected for Tyr AMPylation did not include either the peak at m/z 348.1, or fragments with a mass shift of –347 Da. The results described in this paper highlight a series of diagnostic ions, which can be used not only to confidently identify the AMPylation site based on MS and MS/MS data, but also to selectively scan AMPylated peptides in complex protein mixtures.     

Two-dimensional paper networks: programmable fluidic disconnects for multi-step processes in shaped paper

Most laboratory assays take advantage of multi-step protocols to achieve high performance, but conventional paper-based tests (e.g., lateral flow tests) are generally limited to assays that can be carried out in a single fluidic step. We have developed two-dimensional paper networks (2DPNs) that use materials from lateral flow tests but reconfigure them to enable programming of multi-step reagent delivery sequences. The 2DPN uses multiple converging fluid inlets to control the arrival time of each fluid to a detection zone or reaction zone, and it requires a method to disconnect each fluid source in a corresponding timed sequence. Here, we present a method that allows programmed disconnection of fluid sources required for multi-step delivery. A 2DPN with legs of different lengths is inserted into a shared buffer well, and the dropping fluid surface disconnects each leg at in a programmable sequence. This approach could enable multi-step laboratory assays to be converted into simple point-of-care devices that have high performance yet remain easy to use.     

Stability of some versions of the Prékopa–Leindler inequality

We study the behavior of positive solutions of the following Dirichlet problem

$$\left \{ \begin{array}{ll} -\Delta_{p}u=\lambda u^{s-1}+u^{q-1} &\quad {\rm in}\enspace \Omega \\ u_{\mid\partial \Omega}=0 \end{array}\right. $$

when s → p ^?. Here \({p >1 , s\,{\in}\,]1,p]}\) and q > p with \({q\leq\frac{Np}{N-p}}\) if N > p.

     

Minimal antiderivatives and monotonicity

We consider settings in convex analysis which give rise to families of convex functions that contain their lower envelope. Given certain partial data regarding a subdifferential, we consider the family of all convex antiderivatives that comply with the given data. We prove that this family is not empty and, in particular, contains a minimal antiderivative under a fairly general assumption on the given data. It turns out that the representation of monotone operators by convex functions fits naturally in these settings. Duality properties of representing functions are also captured by these settings, and the gap between the Fitzpatrick function and the Fitzpatrick family is filled by this broader sense of minimality of the Fitzpatrick function.     

The Inverse Commutant Lifting Problem. I: Coordinate-Free Formalism

It is known that the set of all solutions of a commutant lifting and other interpolation problems admits a Redheffer linear-fractional parametrization. The method of unitary coupling identifies solutions of the lifting problem with minimal unitary extensions of a partially defined isometry constructed explicitly from the problem data. A special role is played by a particular unitary extension, called the central or universal unitary extension. The coefficient matrix for the Redheffer linear-fractional map has a simple expression in terms of the universal unitary extension. The universal unitary extension can be seen as a unitary coupling of four unitary operators (two bilateral shift operators together with two unitary operators coming from the problem data) which has special geometric structure. We use this special geometric structure to obtain an inverse theorem (Theorem 8.4) which characterizes the coefficient matrices for a Redheffer linear-fractional map arising in this way from a lifting problem. The main tool is the formalism of unitary scattering systems developed in Boiko et al. (Operator theory, system theory and related topics (Beer-Sheva/Rehovot 1997), pp. 89–138, 2001) and Kheifets (Interpolation theory, systems theory and related topics, pp. 287–317, 2002)     

The reduction of Ag+ in metallic silver on pseudomelanin films allows for antibacterial activity but does not imply unpaired electrons

Dopamine-melanin films produced through the oxidation of dopamine in the presence of oxygen as an oxidant allow to reduce silver ions onto silver particles as already described in the paper by Lee et al. (H. Lee, S.M. Dellatore, W.M. Miller, P.B. Messersmith, Science 318 (2007) 426.). This reduction process has to occur through the oxidation of moieties present in the melanin film. This investigation shows that the free radicals present in the pseudomelanin film, quantified by means of electron spin resonance spectroscopy (ESR) for the first time, are not used in the transformation of Ag(+) cations to deposit silver. The ESR signal is hardly affected by the deposition of silver particles. On the other hand, X-ray photoelectron spectroscopy shows a small increase in the density of quinone groups and a small decrease of catechol groups on the surface of the film during the deposition of silver. This suggests that the deposited pseudomelanin films contain a significant fraction of catechol groups able to trigger reduction processes of metallic cations. These silver nanoparticles remain adherent to the melanin films and allow for a quantitative killing of Escherichia coli over a broad range of bacterial dilutions. However, the presence of the bacteria induces a release of the nanoparticles. The pseudomelanin films cannot be reused again for a silver ion reduction step. Nevertheless, the easy preparation of the pseudomelanin-silver composite and its effective one shot bacterial killing activity renders the strategy presented in this paper attractive. Some fundamental questions about redox process allowed by the pseudomelanin films will also be asked.     

Orientability and Energy Minimization in Liquid Crystal Models

Uniaxial nematic liquid crystals are modelled in the Oseen–Frank theory through a unit vector field n. This theory has the apparent drawback that it does not respect the head-to-tail symmetry in which n should be equivalent to ?n. This symmetry is preserved in the constrained Landau–de Gennes theory that works with the tensor \({Q=s \left(n\otimes n-\frac{1}{3} Id\right)}\). We study the differences and the overlaps between the two theories. These depend on the regularity class used as well as on the topology of the underlying domain. We show that for simply-connected domains and in the natural energy class W^1,2 the two theories coincide, but otherwise there can be differences between the two theories, which we identify. In the case of planar domains with holes and various boundary conditions, for the simplest form of the energy functional, we completely characterise the instances in which the predictions of the constrained Landau–de Gennes theory differ from those of the Oseen–Frank theory.     

Cyclic triamines as potential high energy materials. Thermochemical properties of triaziridine and triazirine

As part of our survey of potential high-energy materials, we are considering molecules that have relatively high nitrogen content. Such molecules can decompose or combust to make very stable products. Here, we present calculated thermochemical properties of two molecules containing three nitrogen atoms in a ring: triaziridine and triazirine . Gaussian-2 and -3, CBS-APNO, and CBS-QB3 are the high-precision methods used in this study.     

The discrete coagulation-fragmentation equations: Existence,uniqueness, and density conservation

The discrete coagulation-fragmentation equation describes the kinetics of cluster growth in which clusters can coagulate via binary interactions to form larger clusters or fragment to form smaller ones. These models have many applications in pure and applied science ranging from cluster formation in galaxies to the kinetics of phase transformations in binary alloys. Our results relate to existence, uniqueness, density conservation and continuous dependence and they generalise the corresponding results in [ref. 2] for the Becker-Doring equations for which the processes are restricted to clusters gaining or shedding one particle. Examples are given which illustrate the role of the assumptions on the kinetic coefficients and show the rich set of analytic phenomena supported by the general discrete coagulation-fragmentation equations.