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We study a theoretical model for the toxin-antitoxin (hok/sok) mechanism for plasmid maintenance in bacteria. Toxin-antitoxin systems enforce the maintenance of a plasmid through post-segregational killing of cells that have lost the plasmid. Key to their function is the tight regulation of expression of a protein toxin by an sRNA antitoxin. Here, we focus on the nonlinear nature of the regulatory circuit dynamics of the toxin-antitoxin mechanism. The mechanism relies on a transient increase in protein concentration rather than on the steady state of the genetic circuit. Through a systematic analysis of the parameter dependence of this transient increase, we confirm some known design features of this system and identify new ones: for an efficient toxin-antitoxin mechanism, the synthesis rate of the toxin’s mRNA template should be lower that of the sRNA antitoxin, the mRNA template should be more stable than the sRNA antitoxin, and the mRNA-sRNA complex should be more stable than the sRNA antitoxin. Moreover, a short half-life of the protein toxin is also beneficial to the function of the toxin-antitoxin system. In addition, we study a therapeutic scenario in which a competitor mRNA is introduced to sequester the sRNA antitoxin, causing the toxic protein to be expressed.
pH-sensitive nanoparticles have a great potential for dermal and transfollicular drug delivery. In this study, pH-sensitive, dexamethasone-loaded Eudragit (R) L 100, Eudragit (R) L 100-55, Eudragit (R) S 100, HPMCP-50, HPMCP-55 and cellulose acetate phthalate nanoparticles were prepared by nanoprecipitation and characterized. The pH-dependent swelling, erosion, dissolution and drug release kinetics were investigated in vitro using dynamic light scattering and Franz diffusion cells, respectively. Their toxicity potential was assessed by the ROS and MTT assays. 100-700 nm nanoparticles with high drug loading and entrapment efficiency were obtained. The nanoparticles bear no toxicity potential. Cellulose phthalates nanoparticles were more sensitive to pH than acrylates nanoparticles. They dissolved in 10 mM pH 7.5 buffer and released > 80% of the drug within 7 h. The acrylate nanoparticles dissolved in 40 mM pH 7.5 buffer and released 65-70% of the drug within 7 h. The nanoparticles remained intact in 10 and 40 mM pH 6.0 buffers (HPMCP nanoparticles dissolved in 40 mM pH 6.0 buffer) and released slowly. The nanoparticles properties could be modulated by blending the different polymers. In conclusion, various pH-sensitive nanoparticles that could release differently on the skin surface and dissolve and release in the hair follicles were obtained.
Advances in nanotechnology lead to an increasing interest in how nanoparticles interact with biomembranes. Nanoparticles are wrapped spontaneously by biomembranes if the adhesive interactions between the particles and membranes compensate for the cost of membrane bending. In the last years, the cooperative wrapping of spherical nanoparticles in membrane tubules has been observed in experiments and simulations. For spherical nanoparticles, the stability of the particle-filled membrane tubules strongly depends on the range of the adhesive particle-membrane interactions. In this article, it is shown via modeling and energy minimization that elongated and patchy particles are wrapped cooperatively in membrane tubules that are highly stable for all ranges of the particle-membrane interactions, compared to individual wrapping of the particles. The cooperative wrapping of linear chains of elongated or patchy particles in membrane tubules may thus provide an efficient route to induce membrane tubulation, or to store such particles in membranes.
Halloysites as tubular alumosilicates are introduced as inexpensive natural nanoparticles to form and stabilize oil-water emulsions. This stabilized emulsion is shown to enable efficient interfacial catalytic reactions. Yield, selectivity, and product separation can be tremendously enhanced, e.g., for the hydroformylation reaction of dodecene to tridecanal. In perspective, this type of formulation may be used for oil spill dispersions. The key elements of the described formulations are clay nanotubes (halloysites) which are highly anisometric, can be filled by helper molecules, and are abundantly available in thousands of tons, making this technology scalable for industrial applications.
This study introduces a thermally responsive, polymer-based electrode system. The key component is a surface-attached, temperature-responsive poly(oligoethylene glycol) methacrylate (poly(OEGMA)) type polymer bearing photoreactive benzophenone and carboxy groups containing side chains. The responsive behavior of the polymer in aqueous media has been investigated by turbidimetry measurements. Polymer films are formed on gold substrates by means of the photoreactive 2(dicyclohexylphosphino)benzophenone (DPBP) through photocrosslinking. The electrochemical behavior of the resulting polymer-substrate interface has been investigated in buffered [Fe(CN)6](3-)/[Fe (CN)6](4-)solutions at room temperature and under temperature variation by cyclic voltammetry (CV). The CV experiments show that with increasing temperature structural changes of the polymer layer occur, which alter the output of the electrochemical measurement. Repeated heating/cooling cycles analyzed by CV measurements and pH changes analyzed by quartz crystal microbalance with dissipation monitoring (QCM-D) reveal the reversible nature of the restructuring process. The immobilized films are further modified by covalent coupling of two small biomolecules - a hydrophobic peptide and a more hydrophilic one. These attached components influence the hydrophobicity of the layer in a different way the resulting change of the temperature-caused behavior has been studied by CV indicating a different state of the polymer after coupling of the hydrophobic peptide.
The absorption of TeV gamma-ray photons produced in relativistic jets by surrounding soft photon fields is a long-standing problem of jet physics. In some cases, the most likely emission site close to the central black hole is ruled out because of the high opacity caused by strong optical and infrared photon sources, such as the broad-line region. Mostly neglected for jet modelling is the absorption of gamma-rays in the starlight photon field of the host galaxy. Analysing the absorption for arbitrary locations and observation angles of the gamma-ray emission site within the host galaxy, we find that the distance to the galaxy centre, the observation angle, and the distribution of starlight in the galaxy are crucial for the amount of absorption. We derive the absorption value for a sample of 20 TeV-detected blazars with a redshift z(r) < 0.2. The absorption value of the gamma-ray emission located in the galaxy centre may be as high as 20 per cent, with an average value of 6 per cent. This is important in order to determine the intrinsic blazar parameters. We see no significant trends in our sample between the degree of absorption and host properties, such as starlight emissivity, galactic size, half-light radius, and redshift. While the uncertainty of the spectral properties of the extragalactic background light exceeds the effect of absorption by stellar light from the host galaxy in distant objects, the latter is a dominant effect in nearby sources. It may also be revealed in a differential comparison of sources with similar redshifts.
The transcriptional regulator MINIYO (IYO) is essential and rate-limiting for initiating cell differentiation in Arabidopsis thaliana. Moreover, IYO moves from the cytosol into the nucleus in cells at the meristem periphery, possibly triggering their differentiation. However, the genetic mechanisms controlling IYO nuclear accumulation were unknown, and the evidence that increased nuclear IYO levels trigger differentiation remained correlative. Searching for IYO interactors, we identified RPAP2 IYO Mate (RIMA), a homolog of yeast and human proteins linked to nuclear import of selective cargo. Knockdown of RIMA causes delayed onset of cell differentiation, phenocopying the effects of IYO knockdown at the transcriptomic and developmental levels. Moreover, differentiation is completely blocked when IYO and RIMA activities are simultaneously reduced and is synergistically accelerated when IYO and RIMA are concurrently overexpressed, confirming their functional interaction. Indeed, RIMA knockdown reduces the nuclear levels of IYO and prevents its prodifferentiation activity, supporting the conclusion that RIMA-dependent nuclear IYO accumulation triggers cell differentiation in Arabidopsis. Importantly, by analyzing the effect of the IYO/RIMA pathway on xylem pole pericycle cells, we provide compelling evidence reinforcing the view that the capacity for de novo organogenesis and regeneration from mature plant tissues can reside in stem cell reservoirs.
Chemotactic motion in a chemical gradient is an essential cellular function that controls many processes in the living world. For a better understanding and more detailed modelling of the underlying mechanisms of chemotaxis, quantitative investigations in controlled environments are needed. We developed a setup that allows us to separately address the dependencies of the chemotactic motion on the average background concentration and on the gradient steepness of the chemoattractant. In particular, both the background concentration and the gradient steepness can be kept constant at the position of the cell while it moves along in the gradient direction. This is achieved by generating a well-defined chemoattractant gradient using flow photolysis. In this approach, the chemoattractant is released by a light-induced reaction from a caged precursor in a microfluidic flow chamber upstream of the cell. The flow photolysis approach is combined with an automated real-time cell tracker that determines changes in the cell position and triggers movement of the microscope stage such that the cell motion is compensated and the cell remains at the same position in the gradient profile. The gradient profile can be either determined experimentally using a caged fluorescent dye or may be alternatively determined by numerical solutions of the corresponding physical model. To demonstrate the function of this adaptive microfluidic gradient generator, we compare the chemotactic motion of Dictyostelium discoideum cells in a static gradient and in a gradient that adapts to the position of the moving cell. Published by AIP Publishing.
In 1997, Henry Lieberman stated that debugging is the dirty little secret of computer science. Since then, several promising debugging technologies have been developed such as back-in-time debuggers and automatic fault localization methods. However, the last study about the state-of-the-art in debugging is still more than 15 years old and so it is not clear whether these new approaches have been applied in practice or not. For that reason, we investigate the current state of debugging in a comprehensive study. First, we review the available literature and learn about current approaches and study results. Second, we observe several professional developers while debugging and interview them about their experiences. Third, we create a questionnaire that serves as the basis for a larger online debugging survey. Based on these results, we present new insights into debugging practice that help to suggest new directions for future research.
Introduction Methods A commercial Real Time Location System was adapted to meet these requirements and subsequently validated in three households by monitoring various bathroom behaviours. Results The results indicate that the system is robust, can monitor behaviours over the long-term in different households and can reliably distinguish between individuals. Precision rates were high and consistent. Recall rates were less consistent across households and behaviours, although recall rates improved considerably with practice at set-up of the system. The achieved precision and recall rates were comparable to the rates observed in more controlled environments using more valid methods of ground truthing. Conclusion These initial findings indicate that the system is a valuable, flexible and robust system for monitoring behaviour in its natural environment that would allow new research questions to be addressed.
The polar and subtropical jet streams are strong upper-level winds with a crucial influence on weather throughout the Northern Hemisphere midlatitudes. In particular, the polar jet is located between cold arctic air to the north and warmer subtropical air to the south. Strongly meandering states therefore often lead to extreme surface weather. The parameter values of the detection scheme are optimized using simulated annealing and a skill function that accounts for the zonal-mean jet stream position (Rikus, 2015). After the successful optimization process, we apply our scheme to reanalysis data covering 1979-2015 and calculate seasonal-mean probabilistic maps and trends in wind strength and position of jet streams. We present longitudinally defined probability distributions of the positions for both jets for all on the Northern Hemisphere seasons. This shows that winter is characterized by two well-separated jets over Europe and Asia (ca. 20 degrees W to 140 degrees E). In contrast, summer normally has a single merged jet over the western hemisphere but can have both merged and separated jet states in the eastern hemisphere.
In order to modulate the emission of BODIPY fluorophores, they were connected to a diarylethene (DAE) photoswitch via phenylene-ethynylene linkers of different lengths and orientations. The latter allowed for modulation of the electronic coupling in the prepared four BODIPY-DAE dyads, which were compared also to appropriate BODIPY and DAE model compounds by steady state as well as time-resolved spectroscopies. In their open isomers, all dyads show comparable luminescence behavior indicative of an unperturbed BODIPY fluorophore. In strong contrast, in the closed isomers the BODIPY emission is efficiently quenched but the deactivation mechanism depends on the nature of the linker. The most promising dyad was rendered water-soluble by means of micellar encapsulation and aqueous suspensions were investigated by fluorescence spectroscopy and microscopy. Our results (i) illustrate that the electronic communication between the BODIPY and DAE units can indeed be fine-tuned by the nature of the linker to achieve fluorescence modulation while maintaining photoswitchability and (ii) highlight potential applications to image and control biological processes with high spatio-temporal resolution.
In 2010, project CoCoCo (incipient COntinent-COntinent COllision) recorded a 650 km long amphibian N-S wide-angle seismic profile, extending from the Anatolian plateau across southern Turkey and Cyprus to just south of the Eratosthenes Seamount (ESM). The aim of the project is to reveal the impact of the transition from subduction to continent-continent collision of Africa with Anatolia. Arrival picking, finite-differences ray-tracing and inversion of the offshore and on-offshore data produced a tomographic model across southern Cyprus, the accretionary wedge and the ESM. The main features of this model are (1) crustal P-velocities predominantly lower than 6.5 km/s beneath the ESM, (2) crustal thickness between 28 and 37 km, (3) an upper crustal reflection at 5 km depth beneath the ESM, (4) the likely presence of oceanic crust south of the ESM and a transform margin north of it and (5) a 12 km thick ophiolite sequence on Cyprus. Land shots on Turkey, also recorded on Cyprus, gravity data and geological and previous seismic investigations allow to derive a layered velocity model beneath Anatolia and the northern part of Cyprus. The main features of this model are (1) Moho depths of 38–45 km beneath the Anatolian plateau, (2) an upper and lower crust with large lateral changes in velocity and thickness, (3) a north-dipping subducting plate below Cyprus with a steepening of the dip-angle of the plate at about 45 km depth. Thus, the wide-angle seismic and gravity data provide detailed insights into the 2-D geometry and velocity structures associated with the Cyprus Arc collision zone. Finally, integrated analysis of the geophysics and geology allows a comprehensive interpretation of the crustal structure related to the collision process.
The potassium channel AKT2 plays important roles in phloem loading and unloading. It can operate as inward-rectifying channel that allows H+-ATPase-energized K+ uptake. Moreover, through reversible post-translational modifications it can also function as an open, K+-selective channel, which taps a ‘potassium battery’, providing additional energy for transmembrane transport processes. Knowledge about proteins involved in the regulation of the operational mode of AKT2 is very limited. Here, we employed a large-scale yeast two-hybrid screen in combination with fluorescence tagging and null-allele mutant phenotype analysis and identified the plasma membrane localized receptor-like kinase MRH1/MDIS2 (AT4G18640) as interaction partner of AKT2. The phenotype of the mrh1-1 knockout plant mirrors that of akt2 knockout plants in energy limiting conditions. Electrophysiological analyses showed that MRH1/MDIS2 failed to exert any functional regulation on AKT2. Using structural protein modeling approaches, we instead gathered evidence that the putative kinase domain of MRH1/MDIS2 lacks essential sites that are indispensable for a functional kinase suggesting that MRH1/MDIS2 is a pseudokinase. We propose that MRH1/MDIS2 and AKT2 are likely parts of a bigger protein complex. MRH1 might help to recruit other, so far unknown partners, which post-translationally regulate AKT2. Additionally, MRH1 might be involved in the recognition of chemical signals.
We study biased Maker-Breaker positional games between two players, one of whom is playing randomly against an opponent with an optimal strategy. In this work we focus on the case of Breaker playing randomly and Maker being "clever". The reverse scenario is treated in a separate paper. We determine the sharp threshold bias of classical games played on the edge set of the complete graph , such as connectivity, perfect matching, Hamiltonicity, and minimum degree-1 and -2. In all of these games, the threshold is equal to the trivial upper bound implied by the number of edges needed for Maker to occupy a winning set. Moreover, we show that CleverMaker can not only win against asymptotically optimal bias, but can do so very fast, wasting only logarithmically many moves (while the winning set sizes are linear in n).
The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
Head and neck squamous cell carcinomas (HNSCC) exhibiting resistance to the EGFR-targeting drug cetuximab poses a challenge to their effective clinical management. Here, we report a specific mechanism of resistance in this setting based upon the presence of a single nucleotide polymorphism encoding EGFR-K-521 (K-allele), which is expressed in > 40% of HNSCC cases. Patients expressing the K-allele showed significantly shorter progressionfree survival upon palliative treatment with cetuximab plus chemotherapy or radiation. In several EGFR-mediated cancer models, cetuximab failed to inhibit downstream signaling or to kill cells harboring a high K-allele frequency. Cetuximab affinity for EGFR-K-521 was reduced slightly, but ligand-mediated EGFR acti-vation was intact. We found a lack of glycan sialyation on EGFR-K-521 that associated with reduced protein stability, suggesting a structural basis for reduced cetuximab efficacy. CetuGEX, an antibody with optimized Fc glycosylation targeting the same epitope as cetuximab, restored HNSCC sensitivity in a manner associated with antibody-dependent cellular cytotoxicity rather than EGFR pathway inhibition. Overall, our results highlight EGFR-K-521 expression as a key mechanism of cetuximab resistance to evaluate prospectively as a predictive biomarker in HNSCC patients. Further, they offer a preclinical rationale for the use of ADCC-optimized antibodies to treat tumors harboring this EGFR isoform.
Aims Work-anxiety may produce overly negative views of the workplace that impair provider efforts to assess work ability from patient self-report. This study explores the empirical relationships between patient-reported workplace characteristics, work-anxiety, and subjective and objective work ability measures. Methods 125 patients in medical rehabilitation before vocational reintegration were interviewed concerning their vocational situation, and filled in a questionnaire on work-anxiety, subjective mental work ability and perceived workplace characteristics. Treating physicians gave independent socio-medical judgments concerning the patients’ work ability and impairment, and need for supportive means for vocational reintegration. Results Patients with high work-anxiety reported more negative workplace characteristics. Low judgments of work ability were correlated with problematic workplace characteristics. When controlled for work-anxiety, subjective work ability remained related only with social workplace characteristics and with work achievement demands, but independent from situational or task characteristics. Sick leave duration and physicians’ judgment of work ability were not significantly related to patient-reported workplace characteristics. Conclusions In socio-medical work ability assessments, patients with high work-anxiety may over-report negative workplace characteristics that can confound provider estimates of work ability. Assessing work-anxiety may be important to assess readiness for returning to work and initiating work-directed treatments.
Childhood adversity plays an important role for development of major depressive disorder (MDD). There are differences in subcortical brain structures between patients with MDD and healthy controls, but the specific impact of childhood adversity on such structures in MDD remains unclear. Thus, aim of the present study was to investigate whether childhood adversity is associated with subcortical volumes and how it interacts with a diagnosis of MDD and sex. Within the ENIGMA-MDD network, nine university partner sites, which assessed childhood adversity and magnetic resonance imaging in patients with MDD and controls, took part in the current joint mega-analysis. In this largest effort world-wide to identify subcortical brain structure differences related to childhood adversity, 3036 participants were analyzed for subcortical brain volumes using FreeSurfer. A significant interaction was evident between childhood adversity, MDD diagnosis, sex, and region. Increased exposure to childhood adversity was associated with smaller caudate volumes in females independent of MDD. All subcategories of childhood adversity were negatively associated with caudate volumes in females - in particular emotional neglect and physical neglect (independently from age, ICV, imaging site and MDD diagnosis). There was no interaction effect between childhood adversity and MDD diagnosis on subcortical brain volumes. Childhood adversity is one of the contributors to brain structural abnormalities. It is associated with subcortical brain abnormalities that are relevant to psychiatric disorders such as depression. (C) 2016 Published by Elsevier Ltd.