Generalized disks of contractivity for explicit and implicit Runge-Kutta methods

The A-contractivity of Runge-Kutta methods with respect to an inner product norm was investigated thoroughly by Butcher and Burrage (who used the term B-stability). Their theory is extended to contractivity in a region bounded by a circle through the origin. The largest possible circle is calculated for many known explicit Runge-Kutta methods. As a rule it is considerably smaller than the stability region, and in several cases it degenerates to a point. It is shown that an explicit Runge-Kutta method cannot be contractive in any circle of this class if it is more than fourth order accurate

Application of recombinant TAF3 PHD domain instead of anti-H3K4me3 antibody

BACKGROUND: Histone posttranslational modifications (PTMs) represent a focal point of chromatin regulation. The genome-wide and locus-specific distribution and the presence of distinct histone PTMs is most commonly examined with the application of histone PTM-specific antibodies. In spite of their central role in chromatin research, polyclonal antibodies suffer from disadvantages like batch-to-batch variability and insufficient documentation of their quality and specificity. RESULTS: To mitigate some of the pitfalls of using polyclonal antibodies against H3K4me3, we successfully validated the application of a recombinant TAF3 PHD domain as anti-H3K4me3 affinity reagent in peptide array, western blot and ChIP-like experiments coupled with qPCR and deep sequencing. CONCLUSIONS: The successful addition of the TAF3 PHD domain to the growing catalog of recombinant affinity reagents for histone PTMs could help to improve the reproducibility, interpretation and cross-laboratory validation of chromatin data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13072-016-0061-9) contains supplementary material, which is available to authorized users

Temporal Stream Logic: Synthesis beyond the Bools

Reactive systems that operate in environments with complex data, such as mobile apps or embedded controllers with many sensors, are difficult to synthesize. Synthesis tools usually fail for such systems because the state space resulting from the discretization of the data is too large. We introduce TSL, a new temporal logic that separates control and data. We provide a CEGAR-based synthesis approach for the construction of implementations that are guaranteed to satisfy a TSL specification for all possible instantiations of the data processing functions. TSL provides an attractive trade-off for synthesis. On the one hand, synthesis from TSL, unlike synthesis from standard temporal logics, is undecidable in general. On the other hand, however, synthesis from TSL is scalable, because it is independent of the complexity of the handled data. Among other benchmarks, we have successfully synthesized a music player Android app and a controller for an autonomous vehicle in the Open Race Car Simulator (TORCS.

The Caulobacter crescentus DNA-(adenine-N6)-methyltransferase CcrM methylates DNA in a distributive manner

The specificity and processivity of DNA methyltransferases have important implications regarding their biological functions. We have investigated the sequence specificity of CcrM and show here that the enzyme has a high specificity for GANTC sites, with only minor preferences at the central position. It slightly prefers hemimethylated DNA, which represents the physiological substrate. In a previous work, CcrM was reported to be highly processive [Berdis et al. (1998) Proc. Natl Acad. Sci. USA 95: 2874–2879]. However upon review of this work, we identified a technical error in the setup of a crucial experiment in this publication, which prohibits making any statement about the processivity of CcrM. In this study, we performed a series of in vitro experiments to study CcrM processivity. We show that it distributively methylates six target sites on the pUC19 plasmid as well as two target sites located on a 129-mer DNA fragment both in unmethylated and hemimethylated state. Reaction quenching experiments confirmed the lack of processivity. We conclude that the original statement that CcrM is processive is no longer valid

Calculation of energy release function of focused ion beam in solids

The mathematical formulation of space-time energy release function of accelerated ions in solids is presented. Continuous focused ion beam interaction with metals is considered. The power density of deposited energy and specific energy input in a target has been calculated. A beam energy fraction expended on the collisional sputtering of target atoms has been estimated

Wettable Ceramic-Based Drained Cathode Technology for Aluminum Electrolysis

The goal of the project was to develop the ceramic based materials, technology, and necessary engineering packages to retrofit existing aluminum reduction cells in order to reduce energy consumption required for making primary aluminum. The ceramic materials would be used in a drained cathode configuration which would provide a stable, molten aluminum wetted cathode surface, allowing the reduction of the anode-cathode distance, thereby reducing the energy consumption. This multi-tasked project was divided into three major tasks: (1) Manufacturing and laboratory scale testing/evaluation of the ceramic materials, (2) Pilot scale testing of qualified compositions from the first task, and (3) Designing, retrofitting, and testing the ceramic materials in industrial cells at Kaiser Mead plant in Spokane, Washington. Specific description of these major tasks can be found in Appendix A - Project Scope. Due to the power situation in the northwest, the Mead facility was closed, thus preventing the industrial cell testing

Classes of fast and specific search mechanisms for proteins on DNA

Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.Comment: 65 pages, 23 figure

Cytosine-to-Uracil Deamination by SssI DNA Methyltransferase

The prokaryotic DNA(cytosine-5)methyltransferase M.SssI shares the specificity of eukaryotic DNA methyltransferases (CG) and is an important model and experimental tool in the study of eukaryotic DNA methylation. Previously, M.SssI was shown to be able to catalyze deamination of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing from the reaction. To test whether this side-activity of the enzyme can be used to distinguish between unmethylated and C5-methylated cytosines in CG dinucleotides, we re-investigated, using a sensitive genetic reversion assay, the cytosine deaminase activity of M.SssI. Confirming previous results we showed that M.SssI can deaminate cytosine to uracil in a slow reaction in the absence of SAM and that the rate of this reaction can be increased by the SAM analogue 5’-amino-5’-deoxyadenosine. We could not detect M.SssI-catalyzed deamination of C5-methylcytosine (m5C). We found conditions where the rate of M.SssI mediated C-to-U deamination was at least 100-fold higher than the rate of m5C-to-T conversion. Although this difference in reactivities suggests that the enzyme could be used to identify C5-methylated cytosines in the epigenetically important CG dinucleotides, the rate of M.SssI mediated cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction. Amino acid replacements in the presumed SAM binding pocket of M.SssI (F17S and G19D) resulted in greatly reduced methyltransferase activity. The G19D variant showed cytosine deaminase activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase activity was also detectable in an E. coli ung+ host proficient in uracil excision repair

Effects of 192 IgG-saporin on acetylcholinesterase histochemistry in male and female rats

Sex hormones may exert neuroprotective effects in various models of brain lesions. Male and female Long-Evans rats were subjected to intracerebroventricular injections of 2 microg 192 IgG-saporin or vehicle. Starting 2 days before surgery, half the male rats were treated with estradiol for 7 days. Three weeks after surgery, they were sacrificed for histochemical staining of acetylcholinesterase (AChE) and densitometric evaluations. The lesion induced a substantial to dramatic decrease of the AChE-positive fiber density in the cingulate, somatosensory, piriform, retrosplenial and perirhinal cortices, and in the hippocampus. Weak effects were found in the striatum. There was no significant decrease in the dorsal thalamus. Sex had no significant effect on AChE-positive staining in any brain area. In males, estradiol treatment did not alter the effects of 192 IgG-saporin. These results show that sex or estradiol treatment in male rats does not interfere with the immunotoxic effects of intracerebroventricular injections of 192 IgG-saporin on cholinergic projections from the basal forebrain