Nine-amino-acid transactivation domain: Establishment and prediction utilities

AbstractHere we describe the establishment and prediction utilities for a novel nine-amino-acid transactivation domain, 9aa TAD, that is common to the transactivation domains of a large number of yeast and animal transcription factors. We show that the 9aa TAD motif is required for the function of the transactivation domain of Gal4 and the related transcription factors Oaf1 and Pip2. The 9aa TAD possesses an autonomous transactivation activity in yeast and mammalian cells. Using sequence alignment and experimental data we derived a pattern that can be used for 9aa TAD prediction. The pattern allows the identification of 9aa TAD in other Gal4 family members or unrelated yeast, animal, and viral transcription factors. Thus, the 9aa TAD represents the smallest known denominator for a broad range of transcription factors. The wide occurrence of the 9aa TAD suggests that this domain mediates conserved interactions with general transcriptional cofactors. A computational search for the 9aa TAD is available online from National EMBnet-Node Austria at http://www.at.embnet.org/toolbox/9aatad/

Scanning Near-Field Optical Coherent Spectroscopy of Single Molecules at 1.4 Kelvin

We present scanning near-field extinction spectra of single molecules embedded in a solid matrix. By varying the molecule-tip separation, we modify the line shape of the spectra, demonstrating the coherent nature of the interaction between the incident laser light and the excited state of the molecule. We compare the measured data with the outcome of numerical calculations and find a very good agreement.Comment: 3 pages, 5 figures, submitted to Optics Letter

Impact of bio-augmentation with Sphingomonas sp. strain TTNP3 in membrane bioreactors degrading nonylphenol

This study evaluates the potential of bio-augmentation to improve the degradation of recalcitrant nonylphenol during the wastewater treatment in membrane bioreactors (MBR). One MBR containing activated sludge was bio-augmented using multistep inoculation with freeze dried Sphingomonas sp. strain TTNP3, whereas a second control reactor contained activated sludge solely. The 14C-labeled-nonylphenol isomer (4-[1-ethyl-1,3-dimethylpentyl]phenol) was applied as a single pulse. Bio-augmentation resulted in an immediate increase of dissolved radioactivity in the effluent in comparison to the control reactor (13% and 2% of initially applied radioactivity after 1day, respectively). After 5days of operation, the retentate of the bio-augmented reactor contained only 7% of the initial radioactivity in contrast to 50% in the control reactor. The radioactivity associated to the mixed liquor suspended solids, i.e., the suspension of biomass and other solids on the retentate side of the membrane, was mainly found as non-extractable residues that were increasingly formed during prolonged reactor operation, especially for the control MBR. HPLC-LSC and GC-MSn analyses revealed that the bio-augmented reactor produced more polar hydroquinone as main degradation intermediate, whereas the control reactor effluent contained a complex mixture of apolar compounds with shortened oxidized alkyl chains. Thus, the apparent differences in the behavior of nonylphenol between the reactors were due to the catabolism of nonylphenol conferred by bio-augmentation with Sphingomonas sp. strain TTNP

Inter-technique validation of tropospheric slant total delays

An extensive validation of line-of-sight tropospheric slant total delays (STD) from Global Navigation Satellite Systems (GNSS), ray tracing in numerical weather prediction model (NWM) fields and microwave water vapour radiometer (WVR) is presented. Ten GNSS reference stations, including collocated sites, and almost 2 months of data from 2013, including severe weather events were used for comparison. Seven institutions delivered their STDs based on GNSS observations processed using 5 software programs and 11 strategies enabling to compare rather different solutions and to assess the impact of several aspects of the processing strategy. STDs from NWM ray tracing came from three institutions using three different NWMs and ray-tracing software. Inter-techniques evaluations demonstrated a good mutual agreement of various GNSS STD solutions compared to NWM and WVR STDs. The mean bias among GNSS solutions not considering post-fit residuals in STDs was -0.6 mm for STDs scaled in the zenith direction and the mean standard deviation was 3.7 mm. Standard deviations of comparisons between GNSS and NWM ray-tracing solutions were typically 10 mm +/- 2 mm (scaled in the zenith direction), depending on the NWM model and the GNSS station. Comparing GNSS versus WVR STDs reached standard deviations of 12 mm +/- 2 mm also scaled in the zenith direction. Impacts of raw GNSS post-fit residuals and cleaned residuals on optimal reconstructing of GNSS STDs were evaluated at intertechnique comparison and for GNSS at collocated sites. The use of raw post-fit residuals is not generally recommended as they might contain strong systematic effects, as demonstrated in the case of station LDB0. Simplified STDs reconstructed only from estimated GNSS tropospheric parameters, i.e. without applying post-fit residuals, performed the best in all the comparisons; however, it obviously missed part of tropospheric signals due to non-linear temporal and spatial variations in the troposphere. Although the post-fit residuals cleaned of visible systematic errors generally showed a slightly worse performance, they contained significant tropospheric signal on top of the simplified model. They are thus recommended for the reconstruction of STDs, particularly during high variability in the troposphere. Cleaned residuals also showed a stable performance during ordinary days while containing promising information about the troposphere at low-elevation angles.Web of Science1062208218

Cryptic invasion suggested by a cytogeographic analysis of the halophytic Puccinellia distans complex (Poaceae) in Central Europe

Introduction: Despite the wealth of studies dealing with the invasions of alien plants, invasions of alien genotypes of native species (cryptic invasions) have been vastly neglected. The impact of cryptic invasions on the biodiversity of plant communities can, however, be significant. Inland saline habitats and halophytes (i.e., salt-tolerant plant species) are especially threatened by this phenomenon as they inhabit fragmented remnants of largely destroyed habitats, but at the same time some of these halophytic species are rapidly spreading along salt-treated roads. To study potential cryptic invasion of halophytes, the patterns of genome size and ploidy variation in the Puccinellia distans complex (Poaceae), the most rapidly spreading roadside halophyte in Central Europe, were investigated. Methods: DNA flow cytometry with confirmatory chromosome counts were employed to assess ploidy levels of 1414 individuals from 133 populations of the P. distans complex. In addition, climatic niche modelling was used to predict the distributions of selected cytotypes. Results: Eight groups differing in ploidy level and/or genome size were discovered, one diploid (2x; 2n = 14), two tetraploid (4xA, 4xB; 2n = 28), one pentaploid (5x; 2n = 35), three hexaploid (6xA, 6xB, 6xC; 2n = 42), and one heptaploid (7x; 2n = 49). The hexaploids (mostly the 6xC cytotype) were widespread through the study area, spreading intensively in both anthropogenic and natural habitats and probably hybridizing with the natural habitat dwelling tetraploids. In contrast, the non-hexaploid cytotypes rarely spread and were predominantly confined to natural habitats. Discussion: The extensive spread of the hexaploid cytotypes along roadsides has most likely facilitated their incursion into natural habitats. The colonization of new natural habitats by the hexaploids may pose a threat to the indigenous Puccinellia populations by compromising their genetic integrity and/or by outcompeting them

Perspective: The Role of Cryopreservation Techniques in Manufacturing, Transport, and Storage of Car-T Therapy Products

Several clinical trials have proved the efficacy and safety of T-cells chimeric antigen receptor (CAR-T cells) in treatment of malignant lymphoma and the first products were registered in the European Union in 2018. The shelf-life of CAR-T cell products in the liquid state is short, so cryopreservation offers a significant benefit for logistics in manufacturing and patient management. Direct shipment of the cryopreserved CAR-T cell therapy products to the clinical department is feasible, nevertheless, intermediate storage in the hospital cryostorage facility gives significant advantage in planning of their administration to patients. Moreover, some manufacturers prefer transport of the starting material cryopreserved at the collection site. The cryopreservation protocol used for starting material by the authors is based on combining dimethyl sulphoxide (DMSO) with hydroxyethyl starch (HES) and slow controlled cooling in cryobags housed in metal cassettes. This achieves the mononuclear cell post-thaw viability of 98.8 ± 0.5 % and recovery of 72.8, ± 10.2 %. Transport of the starting material to the manufactures and return transport of the CAR-T therapy product is performed by authorized courier companies. Intermediate cryostorage of the final CAR-T cell therapy product is performed in a separate dry-storage liquid nitrogen container. On the day of infusion, the cryopreserved products are transported to the clinical department in a dry shipper. On the wards the product is removed from the cassette, inserted into a sterile plastic bag, thawed in a 37 °C water bath followed by immediate intravenous administration. The authors discuss the adherence of the used technology to good manufacturing practice (GMP) principles and genetic safety assurance rules

Investigation by thermodesorption spectroscopy of hydrogen accumulation features in Zr-1%Nb zirconium alloy during gas-phase hydrogenation

Modern trends in human development require more and more electricity to maintain the pace of economic and scientific development. One of the most environmentally friendly methods of electricity production is the use of nuclear power plants (NPPs). In connection with high impact on structural materials of nuclear power plants cores there is uncontrolled degradation of core material. Understanding the degradation processes will help predict and prevent various man-made disasters. The purpose of this work is to study the accumulation of hydrogen in the zirconium alloy Zr-1%Nb (E110). In this work, we studied the processes of hydrogen sorption and desorption by the zirconium alloy Zr-1%Nb

An Evaluation of Combinations of Lossy Compression and ChangeDetection Approaches. (Technical Report ’15)

Today, time series of numerical data are ubiquitous, for instance in the Internet of Things. In such scenarios, it is often necessary to compress the data and to detect changes on it. More specifically, both methods are used in combination, i.e., data is lossily compressed and later decompressed, and then change detection takes place. There exists a broad variety of compression as well as of change-detection techniques. This calls for a systematic comparison of different combinations of compression and change-detection techniques, for different data sets, together with recommendations on how the values of the various (typically non-linear) parameters should be chosen. This article is such an evaluation. Its design is not trivial, necessitating a number of decisions. We work out the details and the rationale behind our design choices. Next to other results, our study shows that the choice of combinations of change detection and compression algorithm and their parameterization does affect result quality significantly. Our evaluation also indicates that results are highly contingent on the nature of the data.ers specify their privacy requirements as so-called discriminative pairs of secrets, and it perturbs data so that an adversary does not learn about the probability distribution of such pairs. However, deploying the framework on complex data such as time series requires application specific work. This includes a general definition of the representation of secrets in the data. Another issue is that the tradeoff between Pufferfish privacy and utility of the data is largely unexplored in quantitative terms. In this study, we quantify this tradeoff for smart meter data. Such data contains fine-grained time series of power-consumption data from private households. Disseminating such data in an uncontrolled way puts privacy at risk. We investigate how time series of energy consumption data must be transformed to facilitate specifying secrets that Pufferfish can use. We ensure the generality of our study by looking at different information-extraction approaches, such as re-identification and non-intrusive-appliance-load monitoring, in combination with a comprehensive set of secrets. Additionally, we provide quantitative utility results for a real-world application, the so-called local energy market