Enzymatic Conversion of Flavonoids using Bacterial Chalcone Isomerase and Enoate Reductase

Flavonoids are a large group of plant secondary metabolites with a variety of biological properties and are therefore of interest to many scientists, as they can lead to industrially interesting intermediates. The anaerobic gut bacterium Eubacterium ramulus can catabolize flavonoids, but until now, the pathway has not been experimentally confirmed. In the present work, a chalcone isomerase (CHI) and an enoate reductase (ERED) could be identified through whole genome sequencing and gene motif search. These two enzymes were successfully cloned and expressed in Escherichia coli in their active form, even under aerobic conditions. The catabolic pathway of E. ramulus was confirmed by biotransformations of flavanones into dihydrochalcones. The engineered E. coli strain that expresses both enzymes was used for the conversion of several flavanones, underlining the applicability of this biocatalytic cascade reaction.     

Affinity Polymers Tailored for the Protein A Binding Site of Immunoglobulin G Proteins

Rational design in combination with a screening process was used to develop affinity polymers for a specific binding site on the surface of immunoglobulin G (IgG) proteins. The concept starts with the identification of critical amino acid residues on the protein interface and their topological arrangement. Appropriate binding monomers were subsequently synthesized. Together with a sugar monomer (2–5 equiv) for water solubility and a dansyl monomer (0.5 equiv) as a fluorescent label, they were subjected in aqueous solution to linear radical copolymerization in various compositions (e.g., azobisisobutyronitrile (AIBN), homogeneous water/DMF mixtures). After ultrafiltration and lyophilization, colorless dry water‐soluble powders were obtained. NMR spectroscopic and gel permeation chromatography (GPC) characterization indicated molecular weights between 30 and 500 kD and confirmed retention of monomer composition as well as the absence of monomers. In a competitive enzyme‐linked immunosorbent assay (ELISA) screen of the polymer libraries (20–50 members), few copolymers qualified as strong and selective binders for the protein A binding site on the Fc fragment of the antibody. Their monomer composition precisely reflected the critical amino acids found at the interface. The simple combination of a charged and a nonpolar binding monomer sufficed for selective submicromolar IgG recognition by the synthetic polymer. Affinities were confirmed by fluorescence titrations; they increased with decreasing salt load but remained largely unaltered at lowered pH. Other proteins, including those of similar size and isoelectric point (pI), were bound 10–1000 times less tightly. This example indicates that interaction domains in other proteins may also be targeted by synthetic polymers if their comonomer composition reflects the nature and arrangement of amino acid residues on the protein surface.     

Asymptotics of Block Toeplitz Determinants and the Classical Dimer Model

We compute the asymptotics of a block Toeplitz determinant which arises in the classical dimer model for the triangular lattice when considering the monomer-monomer correlation function. The model depends on a parameter interpolating between the square lattice (t = 0) and the triangular lattice (t = 1), and we obtain the asymptotics for 0 < t ≤ 1. For 0 < t < 1 we apply the Szegö Limit Theorem for block Toeplitz determinants. The main difficulty is to evaluate the constant term in the asymptotics, which is generally given only in a rather abstract form.     

Surface reduction of freely floating smectic bubbles

Elongated freely floating smectic bubbles are observed during their relaxation to equilibrium sphere shape. Unlike soap bubbles that perform weakly damped oscillations into equilibrium, this relaxation is overdamped in smectics by internal structure reorganisation processes. The bubble area reduction of centimetre-sized freely floating bubbles with few nanometres film thickness is recorded with high-speed optical imaging in microgravity and analysed quantitatively. We find a nearly linear reduction of the film area with time, driven by capillary forces and inhibited by smectic layer reorganisations. Characteristic times are in the milliseconds range, with little correlation to the film thickness and bubble size. Instead, the homogeneity of the films and the number and sizes of islands of excess layers that spontaneously form on the films appear to have crucial influence on the dynamics. The efficiency of this process sets the time scale of the film area shrinkage. We discuss the limitations of a minimalistic model that captures smectic layer reorganisation processes.     

NIFTy 3 – Numerical Information Field Theory: A Python Framework for Multicomponent Signal Inference on HPC Clusters

NIFTy , “Numerical Information Field Theory,” is a software framework designed to ease the development and implementation of field inference algorithms. Field equations are formulated independently of the underlying spatial geometry allowing the user to focus on the algorithmic design. Under the hood, NIFTy ensures that the discretization of the implemented equations is consistent. This enables the user to prototype an algorithm rapidly in 1D and then apply it to high‐dimensional real‐world problems. This paper introduces NIFTy  3, a major upgrade to the original NIFTy  framework. NIFTy  3 allows the user to run inference algorithms on massively parallel high performance computing clusters without changing the implementation of the field equations. It supports n‐dimensional Cartesian spaces, spherical spaces, power spaces, and product spaces as well as transforms to their harmonic counterparts. Furthermore, NIFTy  3 is able to handle non‐scalar fields, such as vector or tensor fields. The functionality and performance of the software package is demonstrated with example code, which implements a mock inference inspired by a real‐world algorithm from the realm of information field theory. NIFTy  3 is open‐source software available under the GNU General Public License v3 (GPL‐3) at https://gitlab.mpcdf.mpg.de/ift/NIFTy/tree/NIFTy_3 .     

Electronic Finetuning of 8-Methoxy Psoralens by Palladium-Catalyzed Coupling: Acidochromicity and Solvatochromicity

Differently 5-substituted 8-methoxypsoralens can be synthesized by an efficient synthetic route with various cross-coupling methodologies, such as Suzuki, Sonogashira and Heck reaction. Compared to previously synthesized psoralens, thereby promising daylight absorbing compounds as potentially active agents against certain skin diseases can be readily accessed. Extensive investigations of all synthesized psoralen derivatives reveal fluorescence in the solid state as well as several distinctly emissive derivatives in solution. Donor-substituted psoralens exhibit remarkable photophysical properties, such as high fluorescence quantum yields and pronounced emission solvatochromicity and acidochromicity, which were scrutinized by Lippert–Mataga and Stern–Volmer plots. The results indicate that the compounds exceed the limit of visible light, a significant factor for potential applications as an active agent. In addition, (TD)DFT calculations were performed to elucidate the underlying electronic structure and to assign experimentally obtained data.     

Formation of Sim and SimCn clusters by C60 sputtering of Si

The secondary ion mass spectrum of silicon sputtered by high energy C₆₀⁺ ions in sputter equilibrium is found to be dominated by Si clusters and we report the relative yields of Si_m⁺ (1 ≤ m ≤ 15) and various Si_mC_n⁺ clusters (1 ≤ m ≤ 11 for n = 1; 1 ≤ m ≤ 6 for n = 2; 1 ≤ m ≤ 4 for n = 3). The yields of Si_m⁺ clusters up to Si₇⁺ are significant (between 0.1 and 0.6 of the Si⁺ yield) with even numbered clusters Si₄⁺ and Si₆⁺ having the highest probability of formation. The abundances of cluster ions between Si₈⁺ and Si₁₁⁺ are still significant (>1% relative to Si⁺) but drop by a factor of ∼100 between Si₁₁⁺ and Si₁₃⁺. The probability of formation of clusters Si₁₃⁺-Si₁₅⁺ is approximately constant at ∼5 × 10⁻⁴ relative to Si⁺ and rising a little for Si₁₅⁺, but clusters beyond Si₁₅ are not detected (Si_m≥16⁺/Si⁺ < 1 × 10⁻⁴). The probability of formation of Si_m⁺ and Si_mC_n⁺ clusters depends only very weakly on the C₆₀⁺ primary ion energy between 13.5 keV and 37.5 keV. The behaviour of Si_m⁺ and Si_mC_n⁺ cluster ions was also investigated for impacts onto a fresh Si surface to study the effects that saturation of the surface with C₆₀⁺ in reaching sputter equilibrium may have had on the measured abundances. By comparison, there are very minor amounts of pure Si_m⁺ clusters produced during C₆₀⁺ sputtering of silica (SiO₂) and various silicate minerals. The abundances for clusters heavier than Si₂⁺ are very small compared to the case where Si is the target.The data reported here suggest that Si_m⁺ and Si_mC_n⁺ cluster abundances may be consistent in a qualitative way with theoretical modelling by others which predicts each carbon atom to bind with 3-4 Si atoms in the sample. This experimental data may now be used to improve theoretical modelling.     

The importance of cochlear processing for the formation of auditory brainstem and frequency following responses

A model for the generation of auditory brainstem responses (ABR) and frequency following responses (FFRs) is presented. The model is based on the concept introduced by Goldstein and Kiang [J. Acoust. Soc. Am. 30, 107-114 (1958)] that evoked potentials recorded at remote electrodes can theoretically be given by convolution of an elementary unit waveform (unitary response) with the instantaneous discharge rate function for the corresponding unit. In the present study, the nonlinear computational auditory-nerve model recently developed by Heinz et al. [ARLO 2(3), 91-96 (2001)] was used to calculate the instantaneous discharge rate ri(t) for fibers i in the frequency range from 0.1 and 10 kHz. The summed activity across frequency was convolved with a unitary response which is assumed to reflect contributions from different cell populations within the auditory brainstem, recorded at a given pair of electrodes on the scalp. Predicted potential patterns are compared with experimental data for a number of stimulus and level conditions. Clicks, chirps as defined in Dau et al. [J. Acoust. Soc. Am. 107, 1530-1540 (2000)], long-duration stimuli comprising the chirp, as well as tones and slowly varying tonal sweeps were considered. The results demonstrate the importance of considering the effects of the basilar-membrane traveling wave and auditory-nerve processing for the formation of ABR and FFR. Specifically, the results support the hypothesis that the FFR to low-frequency tones represents synchronized activity mainly stemming from mid- and high-frequency units at more basal sites, and not from units tuned to frequencies around the signal frequency.