Tailored Tolane-Perfluorotolane Assembly as Supramolecular Base Pair Replacement in DNA

Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.     

Method development for quantitative monitoring of monoclonal antibodies in upstream cell-culture process samples with limited sample preparation – An evaluation of various capillary coatings

Monoclonal antibodies (mAbs) have become an important class of biopharmaceuticals used for the treatment of various diseases. Their quantification during the manufacturing process is important. In this work, a capillary zone electrophoresis (CZE) method was developed for the monitoring of the mAb concentration during cell-culture processes. CZE method development rules are outlined, particularly discussing various capillary coatings, such as a neutral covalent polyvinyl alcohol coating, a dynamic successive multiple ionic-polymer coating, and dynamic coatings using background electrolyte additives such as triethanolamine (T-EthA) and triethylamine. The dynamic T-EthA coating resulted in most stable electro-osmotic flows and most efficient peak shapes. The method is validated over the range 0.1–10 mg/ml, with a linear range of 0.08–1.3 mg/ml and an extended range of 1–10 mg/ml by diluting samples in the latter concentration range 10-fold in water. The intraday precision and accuracy were 2%–12% and 88%–107%, respectively, and inter-day precision and accuracy were 4%–9% and 93%–104%, respectively. The precision and accuracy of the lowest concentration level (0.08 mg/ml) were slightly worse and still well in scope for monitoring purposes. The presented method proved applicable for analysing in-process cell-culture samples from different cell-culture processes and is possibly well suited as platform method.     

An interlaboratory capillary zone electrophoresis-UV study of various monoclonal antibodies,instruments, and ε-aminocaproic acid lots

Capillary zone electrophoresis ultraviolet (CZE-UV) has become increasingly popular for the charge heterogeneity determination of mAbs and vaccines. The ε-aminocaproic acid (eACA) CZE-UV method has been used as a rapid platform method. However, in the last years, several issues have been observed, for example, loss in electrophoretic resolution or baseline drifts. Evaluating the role of eACA on the reported issues, various laboratories were requested to provide their routinely used eACA CZE-UV methods, and background electrolyte compositions. Although every laboratory claimed to use the He et al. eACA CZE-UV method, most methods actually deviate from He's. Subsequently, a detailed interlaboratory study was designed wherein two commercially available mAbs (Waters’ Mass Check Standard mAb [pI 7] and NISTmAb [pI 9]) were provided to each laboratory, along with two detailed eACA CZE-UV protocols for a short-end, high-speed, and a long-end, high-resolution method. Ten laboratories participated each using their own instruments, and commodities, showing excellence method performance (relative standard deviations [RSDs] of percent time-corrected main peak areas from 0.2% to 1.9%, and RSDs of migration times from 0.7% to 1.8% [n = 50 per laboratory], analysis times in some cases as short as 2.5 min). This study clarified that eACA is not the main reason for the abovementioned variations.     

Anwendung von 2D-NMR-Techniken zur Analyse komplexer Spektren. Maleopimarsäuremethylester

A combination of 2D-NMR-techniques including 2D-J-resolved spectroscopy, SECSY and¹H-¹³C-shift correlation is used to assign the¹H- and¹³C-spectrum of Maleopimaric acid methylester [17,19-Dinoratis-15-ene-4,13,14-tricarboxylic acid 4-methylester, 16-(1-methylethyl)cyclic-13,14-anhydrid (4, 8, 12)] (1).

     

Harmonic divisors and rationality of zeros of Jacobi polynomials

Let $P_{n}^{ ( \alpha,\beta ) } ( x ) $ be the Jacobi polynomial of degree n with parameters α,β. The main result of the paper states the following: If b≠1,3 and c are non-zero relatively prime natural numbers then $P_{n}^{ ( k+ ( d-3 ) /2,k+ ( d-3 ) /2 ) } ( \sqrt{b/c} ) \neq0$ for all natural numbers d,n and $k\in\mathbb{N}_{0}$ . Moreover, under the above assumption, the polynomial $Q ( x ) = \frac{b}{c} ( x_{1}^{2}+\cdots+x_{d-1}^{2} ) + ( \frac{b}{c}-1 ) x_{d}^{2}$ is not a harmonic divisor, and the Dirichlet problem for the cone {Q(x)<0} has polynomial harmonic solutions for polynomial data functions.     

Bound constrained interval global optimization in the COCONUT Environment

We introduce a new interval global optimization method for solving bound constrained problems. The method originates from a small standalone software and is implemented in the COCONUT Environment, a framework designed for the development of complex algorithms, containing numerous state-of-the-art methods in a common software platform. The original algorithm is enhanced by various new methods implemented in COCONUT, regarding both interval function evaluations (such as first and second order derivatives with backward automatic differentiation, slopes, slopes of derivatives, bicentered forms, evaluations on the Karush–John conditions, etc.) and algorithmic elements (inclusion/exclusion boxes, local search, constraint propagation). This resulted in a substantial performance increase as compared to the original code. During the selection of the best combination of options, we performed comparison tests that gave empirical answers to long-lasting algorithmic questions (such as whether to use interval gradients or use slopes instead), that have never been studied numerically in such detail before. The new algorithm, called coco_gop_ex, was tested against the prestigious BARON software on an extensive set of bound constrained problems. We found that in addition to accepting a wider class of bound constrained problems and providing more output information (by locating all global minimizers), coco_gop_ex is competitive with BARON in terms of the solution success rates (with the exception of a set of nonlinear least squares problems), and it often outperforms BARON in running time. In particular, coco_gop_ex was around 21 % faster on average over the set of problems solved by both software systems.     

Splines (with optimal knots) are better

Let S^M _k be the Polynominal splines of degree n-1, and with K segments. If f∈ C ⁿ [a,b],then the distance in the L^p-norm form(0< p ≦ ∞)of from S ^M _k is boundedby M/K ⁿ , with a much smaller M than in similar estimates for other processes of approximation.     

A posteriori error estimates of discontinuous Galerkin methods for non-standard Volterra integro-differential equations

^** Email: jingtang{at}lsec.cc.ac.cn^*** Email: hermann{at}math.mun.ca In this paper we establish a posteriori error estimates forthe discontinuous Galerkin (DG) method applied to linear, semilinearand non-standard (non-linear) Volterra integro-differentialequations. We also present an analysis of the DG method withquadrature for the memory term. Numerical experiments basedon three integro-differential equations are used to illustratevarious aspects of the error analysis.     

Solving stochastic systems with low-rank tensor compression

For parametrised equations, which arise, for example, in equations dependent on random parameters, the solution naturally lives in a tensor product space. The application which we have in mind is a stochastic linear elliptic partial differential equation (SPDE). Usual spatial discretisation leads to a potentially large linear system for each point in the parameter space. Approximating the parametric dependence by a Galerkin ‘ansatz’, the already large number of unknowns—for a fixed parameter value—is multiplied by the dimension of the Galerkin subspace for the parametric dependence, and thus can be very large. Therefore, we try to solve the total system approximately on a smaller submanifold which is found adaptively through compression during the solution process by alternating iteration and compression. We show that for general linearly converging stationary iterative schemes and general adaptation processes—which can be seen as a modification or perturbation of the iteration—the interlaced procedure still converges. Our proposed modification can be used for most stationary solvers for systems on tensor products. We demonstrate this on an example of a discretised SPDE with a simple preconditioned iteration. We choose a truncated singular value decomposition (SVD) for the compression and give details of the implementation, finishing with some examples.