Agent-Based Modeling of Intracellular Transport

We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of vesicles follows a log-normal distribution that changes over time due to fusion processes, their spatial distribution gives rise to distinct patterns. Their occurrence depends on the concentration of proteins which are synthesized based on the transcriptional activities of some genes. Hence, differences in these spatio-temporal vesicle patterns allow indirect conclusions about the (unknown) impact of these genes. By means of agent-based computer simulations we are able to reproduce such patterns on real temporal and spatial scales. Our modeling approach is based on Brownian agents with an internal degree of freedom, $\theta$, that represents the different modes of motion. Conditions inside the cell are modeled by an effective potential that differs for agents dependent on their value $\theta$. Agent's motion in this effective potential is modeled by an overdampted Langevin equation, changes of $\theta$ are modeled as stochastic transitions with values obtained from experiments, and fusion events are modeled as space-dependent stochastic transitions. Our results for the spatio-temporal vesicle patterns can be used for a statistical comparison with experiments. We also derive hypotheses of how the silencing of some genes may affect the intracellular transport, and point to generalizations of the model

Harmonically Resonant Cavity as a Bunch Length Monitor

A compact, harmonically-resonant cavity with a fundamental resonant frequency of 1497 MHz was used to evaluate the temporal characteristics of electron bunches produced by a 130 kV dc high voltage spin-polarized photoelectron source at the Continuous Beam Accelerator Facility (CEBAF) photoinjector, delivered at 249.5 and 499 MHz repetition rates and ranging in width from 45 to 150 picoseconds (FWHM). The cavity’s antenna was attached directly to a sampling oscilloscope that detected the electron bunches as they passed through the cavity bore with a sensitivity of ~ mV/ μA. The oscilloscope wave-forms are a superposition of the harmonic modes excited by the beam, with each cavity mode representing a term of the Fourier series of the electron bunch train. Relatively straitforward post-processing of the waveforms provided a near-real time representation of the electron bunches revealing bunchlength and the relative phasing of interleaved beams. The non-invasive measurements from the harmonically-resonant cavity were compared to measurements obtained using an invasive rf-deflector-cavity technique and to predictions from particle tracking simulations

Nothing moves a surface: vacancy mediated surface diffusion

We report scanning tunneling microscopy observations, which imply that all atoms in a close-packed copper surface move frequently, even at room temperature. Using a low density of embedded indium `tracer' atoms, we visualize the diffusive motion of surface atoms. Surprisingly, the indium atoms seem to make concerted, long jumps. Responsible for this motion is an ultra-low density of surface vacancies, diffusing rapidly within the surface. This interpretation is supported by a detailed analysis of the displacement distribution of the indium atoms, which reveals a shape characteristic for the vacancy mediated diffusion mechanism that we propose.Comment: 4 pages; for associated movie, see http://www-lion.leidenuniv.nl/sections/cm/groups/interface/projects/therm

A genome-wide RNAi screen identifies factors required for distinct stages of C-elegans piRNA biogenesis

In animals, piRNAs and their associated Piwi proteins guard germ cell genomes against mobile genetic elements via an RNAi-like mechanism. In Caenorhabditis elegans, 21U-RNAs comprise the piRNA class, and these collaborate with 22G RNAs via unclear mechanisms to discriminate self from nonself and selectively and heritably silence the latter. Recent work indicates that 21U-RNAs are post-transcriptional processing products of individual transcription units that produce similar to 26-nucleotide capped precursors. However, nothing is known of how the expression of precursors is controlled or how primary transcripts give rise to mature small RNAs. We conducted a genome-wide RNAi screen to identify components of the 21U biogenesis machinery. Screening by direct, quantitative PCR (qPCR)-based measurements of mature 21U-RNA levels, we identified 22 genes important for 21U-RNA production, termed TOFUs (Twenty-One-u Fouled Ups). We also identified seven genes that normally repress 21U production. By measuring mature 21U-RNA and precursor levels for the seven strongest hits from the screen, we assigned factors to discrete stages of 21U-RNA production. Our work identifies for the first time factors separately required for the transcription of 21U precursors and the processing of these precursors into mature 21U-RNAs, thereby providing a resource for studying the biogenesis of this important small RNA class

Dnmt2-dependent methylomes lack defined DNA methylation patterns

Several organisms have retained methyltransferase 2 (Dnmt2) as their only candidate DNA methyltransferase gene. However, information about Dnmt2-dependent methylation patterns has been limited to a few isolated loci and the results have been discussed controversially. In addition, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which raised the possibility that Dnmt2-only genomes might be unmethylated. We have now used whole-genome bisulfite sequencing to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Our results show that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in Dnmt2-deficient flies. Furthermore, genetically modified Dnmt2-only mouse embryonic stem cells lost the DNA methylation patterns found in wild-type cells. Our results thus uncover fundamental differences among animal methylomes and suggest that DNA methylation is dispensable for a considerable number of eukaryotic organisms

Regulation of Peroxisome Proliferator-Activated Receptors by E6-Associated Protein

Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors (NRs) that regulate genes involved in lipid and glucose metabolism. PPAR activity is regulated by interactions with cofactors and of interest are cofactors with ubiquitin ligase activity. The E6-associated protein (E6-AP) is an E3 ubiquitin ligase that affects the activity of other NRs, although its effects on PPARs have not been examined. E6-AP inhibited the ligand-independent transcriptional activity of PPARα and PPARβ, with marginal effects on PPARγ, and decreased basal mRNA levels of PPARα target genes. Inhibition of PPARα activity required the ubiquitin ligase function of E6-AP, but occurred in a proteasome-independent manner. PPARα interacted with E6-AP, and in mice treated with PPARα agonist clofibrate, mRNA and protein levels of E6-AP were increased in wildtype, but not in PPARα null mice, indicating a PPARα-dependent regulation. These studies suggest coordinate regulation of E6-AP and PPARα, and contribute to our understanding of the role of PPARs in cellular metabolism

Experiências de contacto dos bebés com a linguagem escrita

The purpose of this study is to characterize the literacy experiences ofbabies aged between 14 and 24 months. In this study, four issues were analysed: which type of written language experiences are offered to the children, how parents value these literacy experiences, the way parents perceive their own role in the literacy development of their children and what parents know about their means of contributing to the literacy development of their children. Six mothers were interviewed. These interviews were analysed with the use of a categorical content analysis. The results suggest that mothers value and include in their practices facilitative and mediation actions of literacy experiences with their children, noting some variability depending on the respective qualifications.Este estudo exploratório visa descrever as experiências de literacia de bebés entre os 14 e os 25 meses. Analisamse quatro questões, que experiências envolvendo a linguagem escrita no seio familiar são proporcionadas aos bebés, qual o valor que os pais lhes atribuem, como percepcionam o seu papel na promoção do desenvolvimento literácito dos filhos e como podem contribuir para o desenvolvimento da literacia dos mesmos. Adotou-se uma metodologia qualitativa, com recurso à análise de conteúdo categorial das respostas dadas por seis mães em entrevista individual e semiestruturada. Concluiu-se que estas mães valorizam e incluem nas suas práticas ações facilitadoras e de mediação de experiências de literacia por parte dos seus bebés, notando-se alguma variabilidade em função das respetivas habilitações académicas.(undefined)info:eu-repo/semantics/publishedVersio

Development of a lightweight, light-trapped, thin GaAs solar cell for spacecraft applications

This paper describes ultra-lightweight, high performance, thin, light trapping GaAs solar cells for advanced space power systems. The device designs can achieve 24.5 percent efficiency at AMO and 1X conditions, corresponding to a power density of 330 W/m2. A significant breakthrough lies in the potential for a specific power of 2906 W/kg because the entire device is less than 1.5 microns thick. This represents a 440 percent improvement over conventional 4-mil silicon solar cells. In addition to being lightweight, this thin device design can result in increased radiation tolerance. The attachment of the cover glass support to the front surface has been demonstrated by both silicone and electrostatic bonding techniques. Device parameters of 1.002 volts open-circuit voltage, 80 percent fill factor, and a short-circuit current of 24.3 mA/sq cm have been obtained. This demonstrates a conversion efficiency of 14.4 percent resulting in a specific power of 2240 W/kg. Additionally, this new technology offers an alternative approach for enabling multi-bandgap solar cells and high output space solar power devices. The thin device structure can be applied to any 3-5 based solar cell application, yielding both an increase in specific power and radiation tolerance

Semiquantitative assessment of subchondral bone marrow edema-like lesions and subchondral cysts of the knee at 3T MRI: A comparison between intermediate-weighted fat-suppressed spin echo and Dual Echo Steady State sequences

Background\ud Choice of appropriate MR pulse sequence is important for any research studies using imaging-derived data. The aim of this study was to compare semiquantitative assessment of subchondral bone marrow edema-like lesions and subchondral cysts using intermediate-weighted (IW) fat-suppressed (fs) spin echo and Dual Echo Steady State (DESS) sequences on 3 T MRI.\ud \ud Methods\ud Included were 201 subjects aged 35-65 with frequent knee pain. 3T MRI was performed with the same sequence protocol as in the Osteoarthritis Initiative (OAI). In a primary reading subchondral bone marrow edema-like lesions were assessed according to the WORMS system. Two hundred subregions with such lesions were randomly chosen. The extent of subchondral bone marrow edema-like lesions was re-evaluated separately using sagittal IW fs and DESS sequences according to WORMS. Lesion size and confidence of the differentiation between subchondral bone marrow edema-like lesions and subchondral cysts located within or adjacent to them was rated from 0 to 3. Wilcoxon signed-rank tests and chi-square statistics were used to examine differences between the two sequences.\ud \ud Results\ud Of 200 subchondral bone marrow edema-like lesions detected by IW fs sequence, 93 lesions (46.5%) were not depicted by the DESS sequence. The IW fs sequence depicted subchondral bone marrow edema-like lesions to a larger extent than DESS (p < 0.0001), and the opposite was true for subchondral cysts. Confidence scores for differentiation of the two types of lesions were not significantly different between the two sequences.\ud \ud Conclusions\ud In direct comparison the IW fs sequence depicts more subchondral bone marrow edema-like lesions and better demonstrate the extent of their maximum size. The DESS sequence helps in the differentiation of subchondral bone marrow edema-like lesions and subchondral cysts. The IW fs sequence should be used for determination of lesion extent whenever the size of subchondral bone marrow edema-like lesions is the focus of attention