Argument Roles in Adult and Child Comprehension

Language comprehension requires comprehenders to commit rapidly to interpretations based on incremental and occasionally misleading input. This is especially difficult in the case of argument roles, which may be more or less useful depending on whether comprehenders also have access to verb information. In children, a combination of subject-as-agent parsing biases and difficulty with revising initial misinterpretations may be the source of persistent misunderstandings of passives, in which subjects are not agents. My experimental investigation contrasted German five-year-olds’ argument role assignment in passives in a task that combined act-out and eye-tracking measures. Manipulating the order of subject and voice (Exp. 4.1, 4.3) did not impact German learners’ success in comprehending passives, but providing the cue to voice after the main verb (Exp. 4.2) led to a steep drop in children’s comprehension outcomes, suggesting that the inclusion of verb information impacts how young comprehenders process argument role information. In adults, many studies have found that although argument role reversals create strong contrasts in offline cloze probability, they do not elicit N400 contrasts. This may be because in the absence of a main verb, the parser is unable to use argument role information. In an EEG experiment (Exp. 5.1), we used word order to manipulate the presence or absence of verb information, contrasting noun-noun-verb reversals (NNV; which cowboy the bull had ridden) with noun-verb-noun reversals (NVN; which horse had raced the jockey). We found an N400 contrast in NVN contexts, as predicted, but surprisingly, we also found an N400 contrast in NNV contexts. Unlike previous experimental materials, our stimuli were designed to elicit symmetrically strong and distinct verb predictions with both canonical and reversed argument role assignments. These data suggest that adult comprehenders are able to overcome the absence of a main verb when probability distributions over combined verb-argument role information can contribute to generating role-specific verb candidates. The overall investigation suggests that prediction and comprehension of argument role information is impacted by the presence or absence of verb information, which may allow comprehenders to bridge the divide between linguistic representations and world knowledge in real-time processing

Control of replication initiation by the Sum1/Rfm1/Hst1 histone deacetylase

<p>Abstract</p> <p>Background</p> <p>Replication initiation at origins of replication in the yeast genome takes place on chromatin as a template, raising the question how histone modifications, for instance histone acetylation, influence origin firing. Initiation requires binding of the replication initiator, the Origin Recognition Complex (ORC), to a consensus sequence within origins. In addition, other proteins bind to recognition sites in the vicinity of ORC and support initiation. In previous work, we identified Sum1 as an origin-binding protein that contributes to efficient replication initiation. Sum1 is part of the Sum1/Rfm1/Hst1 complex that represses meiotic genes during vegetative growth via histone deacetylation by the histone deacetylase (HDAC) Hst1.</p> <p>Results</p> <p>In this study, we investigated how Sum1 affected replication initiation. We found that it functioned in initiation as a component of the Sum1/Rfm1/Hst1 complex, implying a role for histone deacetylation in origin activity. We identified several origins in the yeast genome whose activity depended on both Sum1 and Hst1. Importantly, <it>sum1</it>Δ or <it>hst1</it>Δ caused a significant increase in histone H4 lysine 5 (H4 K5) acetylation levels, but not other H4 acetylation sites, at those origins. Furthermore, mutation of lysines to glutamines in the H4 tail, which imitates the constantly acetylated state, resulted in a reduction of origin activity comparable to that in the absence of Hst1, showing that deacetylation of H4 was important for full initiation capacity of these origins.</p> <p>Conclusion</p> <p>Taken together, our results demonstrate a role for histone deacetylation in origin activity and reveal a novel aspect of origin regulation by chromatin. These results suggest recruitment of the Sum1/Rfm1/Hst1 complex to a number of yeast origins, where Hst1 deacetylated H4 K5.</p

Modellierung und Simulation des Verhaltens von durchströmten schaltbaren Membranen

Die schaltbare Filtration mithilfe von Hydrogel'=Verbundmembranen zeigt großes Potential zur Lösung einer der grundlegenden Aufgaben in der Humanmedizin: der unkomplizierten und schnellen Analyse von Blutproben zur Erkennung von Unregelmäßigkeiten, wie zum Beispiel zirkulierenden Tumorzellen. In der vorliegenden Arbeit wird ein solches System diskutiert und mithilfe von Methoden des Maschinenwesens -- Modellierung und Simulation -- untersucht. Das betrachtete System besteht aus einer aktiven Hydrogelschicht, welche auf einer passiven Polymerschicht aufgebracht ist und damit eine schaltbare Verbundmembran bildet. Die Arbeit folgt zwei Hauptpfaden: Im festkörpermechanischen Teil werden die mechanischen Aspekte von Verbundmembranen dargestellt, während im fluidmechanischen Teil die Permittivität und Selektivität von Membranen näher beleuchtet werden. Im Folgenden werden Modelle zur Schaltbarkeit ausgehend von aus der Literatur bekannten Ansätzen entwickelt. Diese werden dann im Rahmen von Simulationen -- sowohl im kommerziellen Finite-Elemente-Programm Abaqus, als auch in selbst geschriebenen Matlab-Codes -- umgesetzt. Die vorliegende Arbeit zeigt, dass ein schaltbares System zur Analyse von Zellgrößenprofilen realisierbar und durch Modellierung und Simulation in einem Maß beschreibbar ist, sodass der experimentellen Realisierung nichts mehr im Wege steht.Switchable filtration with hydrogel composite membranes shows great potential to solve one of the basic challenges in life sciences: the fast and easy analysis of blood samples to detect abnormal cells like e.g. circulating tumor cells. In the present work, a system providing these features is discussed using tools provided by engineering: modeling and simulation. The system consists of an active hydrogel composite membrane in combination with a passive polymeric membrane that provides mechanical stability. This forms a switchable composite membrane. The work follows two main paths: In the solid mechanics path, the composition of membranes and their mechanical aspects are discussed. The fluid mechanics path focuses on permittivity and selectivity for particle flows. Originating from the basic concepts of membrane permeation in literature, models for switchability are developed and simulations -- both in the commercial finite-element tool Abaqus and in Matlab scripts -- are performed. The present work proves that the concept of cell-size detection with switchable membranes is suitable for the task. Through the performed simulations, the corresponding processes can be described and designed so that the microfluidic analysis system can be experimentally realized

Characterization of the trp5-27 allele used to monitor drug-induced mitotic gene conversion in the Saccharomyces cerevisiae tester strain D7

Mitotic gene conversions, among other recombinagenic events, can play an important role in the multistep process of carcinogenesis. The ability of chemicals to induce such gene conversions can easily be monitored in the Saccharomyces cerevisiae tester strain YHE2, a derivative of strain D7. For the detection of drug-induced gene conversions, two mutations in the TRP5 locus are used, trp5-12 and trp5-27. Here we report on the characterization of the stable allele trp5-27. Our analysis revealed two relevant mutations in trp5-27: (a) a transition C to T at position 121 after ATG that results in an amber stop codon and abolishes gene expression and (b) a transversion A to T at position 1555 that creates an ochre stop codon. Simultaneous amber and ochre suppression with the suppressors SUP3 and SUP11, respectively, was capable of relieving the tryptophan-requiring phenotype of strains carrying the trp5-27 allele. These findings have implications on the length of gene conversion tracts in conversion events between trp5-12 and trp5-27: conversion tracts can cover several kilobases, if the site of the mutation in trp5-12 lies outside of the positions mutated in trp5-27. Conversely, the maximal length is limited to 1435 bp, if the mutation in trp5-12 is located between the positions mutated in trp5-2

Interactions within the mammalian DNA methyltransferase family

BACKGROUND: In mammals, epigenetic information is established and maintained via the postreplicative methylation of cytosine residues by the DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Dnmt1 is required for maintenance methylation whereas Dnmt3a and Dnmt3b are responsible for de novo methylation. Contrary to Dnmt3a or Dnmt3b, the isolated C-terminal region of Dnmt1 is catalytically inactive, despite the presence of the sequence motifs typical of active DNA methyltransferases. Deletion analysis has revealed that a large part of the N-terminal domain is required for enzymatic activity. RESULTS: The role played by the N-terminal domain in this regulation has been investigated using the yeast two-hybrid system. We show here the presence of an intra-molecular interaction in Dnmt1 but not in Dnmt3a or Dnmt3b. This interaction was confirmed by immunoprecipitation and was localized by deletion mapping. Furthermore, a systematic analysis of interactions among the Dnmt family members has revealed that DNMT3L interacts with the C-terminal domain of Dnmt3a and Dnmt3b. CONCLUSIONS: The lack of methylating ability of the isolated C-terminal domain of Dnmt1 could be explained in part by a physical interaction between N- and C-terminal domains that apparently is required for activation of the catalytic domain. Our deletion analysis suggests that the tertiary structure of Dnmt1 is important in this process rather than a particular sequence motif. Furthermore, the interaction between DNMT3L and the C-terminal domains of Dnmt3a and Dnmt3b suggests a mechanism whereby the enzymatically inactive DNMT3L brings about the methylation of its substrate by recruiting an active methylase

Window-opener as an example for environment measurement and combined actuation of smart hydrogels

An environment is defined by a set of field values, such as temperature, electro-magnetic field, light intensity, air humidity and air composition. Smart materials, such as hydrogels, are able to react to these kinds of stimuli. The spatial and time development of environmental values is governed by transport equations. Hence the reaction, i.e. actuation or sensing, of the smart material can be described based on the same assumptions. The displacement, here swelling and deswelling, of the material depends on the combination of the environmental parameters. Smart materials are called multi-sensitive, when more than one parameter is purposely used (i) to manipulate the material, i.e. as an actuator or (ii) to measure the quantities, i.e. as a (multi-)sensor. However, the material can also perform (iii) the objective of a logic processing unit in addition to (i) and (ii). In the current work, we present a device that realizes this concept: An automatic window opener that senses environmental parameters (light-level and air temperature) and reacts accordingly. The hydrogel material that is included in the simplistic device simultaneously acts as sensor, logic processing unit and actuator

Functional analysis of archaeal MBF1 by complementation studies in yeast

Contains fulltext : 95916.pdf (publisher's version ) (Open Access)BACKGROUND: Multiprotein-bridging factor 1 (MBF1) is a transcriptional co-activator that bridges a sequence-specific activator (basic-leucine zipper (bZIP) like proteins (e.g. Gcn4 in yeast) or steroid/nuclear-hormone receptor family (e.g. FTZ-F1 in insect)) and the TATA-box binding protein (TBP) in Eukaryotes. MBF1 is absent in Bacteria, but is well- conserved in Eukaryotes and Archaea and harbors a C-terminal Cro-like Helix Turn Helix (HTH) domain, which is the only highly conserved, classical HTH domain that is vertically inherited in all Eukaryotes and Archaea. The main structural difference between archaeal MBF1 (aMBF1) and eukaryotic MBF1 is the presence of a Zn ribbon motif in aMBF1. In addition MBF1 interacting activators are absent in the archaeal domain. To study the function and therefore the evolutionary conservation of MBF1 and its single domains complementation studies in yeast (mbf1Delta) as well as domain swap experiments between aMBF1 and yMbf1 were performed. RESULTS: In contrast to previous reports for eukaryotic MBF1 (i.e. Arabidopsis thaliana, insect and human) the two archaeal MBF1 orthologs, TMBF1 from the hyperthermophile Thermoproteus tenax and MMBF1 from the mesophile Methanosarcina mazei were not functional for complementation of an Saccharomyces cerevisiae mutant lacking Mbf1 (mbf1Delta). Of twelve chimeric proteins representing different combinations of the N-terminal, core domain, and the C-terminal extension from yeast and aMBF1, only the chimeric MBF1 comprising the yeast N-terminal and core domain fused to the archaeal C-terminal part was able to restore full wild-type activity of MBF1.However, as reported previously for Bombyx mori, the C-terminal part of yeast Mbf1 was shown to be not essential for function. In addition phylogenetic analyses revealed a common distribution of MBF1 in all Archaea with available genome sequence, except of two of the three Thaumarchaeota; Cenarchaeum symbiosum A and Nitrosopumilus maritimus SCM1. CONCLUSIONS: The absence of MBF1-interacting activators in the archaeal domain, the presence of a Zn ribbon motif in the divergent N-terminal domain of aMBF1 and the complementation experiments using archaeal- yeast chimeric proteins presented here suggests that archaeal MBF1 is not able to functionally interact with the transcription machinery and/or Gcn4 of S. cerevisiae. Based on modeling and structural prediction it is tempting to speculate that aMBF1 might act as a single regulator or non-essential transcription factor, which directly interacts with DNA via the positive charged linker or the basal transcription machinery via its Zn ribbon motif and the HTH domain. However, also alternative functions in ribosome biosynthesis and/or functionality have been discussed and therefore further experiments are required to unravel the function of MBF1 in Archaea

Modeling and simulation of diffusion and reaction processes during the staining of tissue sections on slides

Histological slides are an important tool in the diagnosis of tumors as well as of other diseases that affect cell shapes and distributions. Until now, the research concerning an optimal staining time has been mainly done empirically. In experimental investigations, it is often not possible to stain an already-stained slide with another stain to receive further information. To overcome these challenges, in the present paper a continuum-based model was developed for conducting a virtual (re-)staining of a scanned histological slide. This model is capable of simulating the staining of cell nuclei with the dye hematoxylin (C.I. 75,290). The transport and binding of the dye are modeled (i) along with the resulting RGB intensities (ii). For (i), a coupled diffusion–reaction equation is used and for (ii) Beer–Lambert’s law. For the spatial discretization an approach based on the finite element method (FEM) is used and for the time discretization a finite difference method (FDM). For the validation of the proposed model, frozen sections from human liver biopsies stained with hemalum were used. The staining times were varied so that the development of the staining intensity could be observed over time. The results show that the model is capable of predicting the staining process. The model can therefore be used to perform a virtual (re-)staining of a histological sample. This allows a change of the staining parameters without the need of acquiring an additional sample. The virtual standardization of the staining is the first step towards universal cross-site comparability of histological slides

Permeation control in hydrogel-layered patterned PET membranes with defined switchable pore geometry – Experiments and numerical simulation

AbstractPermeation through polymeric membranes can be controlled by surface coating of a polyethylene terephthalate (PET) membrane with poly(N-isopropylacrylamide) (PNIPAAm) and inserting pores of defined geometry. When the temperature of the system rises above the volume phase transition temperature, the pores open, which allows permeation of formerly blocked particles. The exact control of the temperature allows defined change of the pore size and therefore enables separation abilities. Free swelling experiments are conducted to obtain the swelling behaviour of PNIPAAm. Then, a temperature expansion model is derived in order to simulate this behaviour with the finite element tool ABAQUS. The gained results are in excellent agreement with the observed shape change. Membranes with permeation control of particles can be used for biomedical application in microfluidics to analyse the size distribution of cells or in chemical information processing as a transistor-like component for an information-bearing chemical species. The possibility to simulate the behaviour of such permeation systems allows computer aided design and prediction of permeation abilities in these areas