DNA methylation in Dictyostelium discoideum

DNA methyltransferases of type Dnmt2 are a highly conserved protein family with enigmatic function. The aim of this work was to characterize DnmA, the Dnmt2 methyltransferase in Dictyostelium discoideum, and further to investigate its implication in DNA methylation and transcriptional gene silencing. The genome of the social amoeba Dictyostelium encodes DnmA as the sole DNA methyltransferase. The enzyme bears all ten characteristic DNA methyltransferase motifs in its catalytic domain. The DnmA mRNA was found by RT-PCR to be expressed during vegetative growth and down regulated during development. Investigations using fluorescence microscopy showed that both DnmA-myc and DnmA-GFP fusions predominantly localised to the nucleus. The function of DnmA remained initially unclear, but later experiment revealed that the enzyme is an active DNA methyltransferase responsible for all DNA (cytosine) methylation in Dictyostelium. Neither in gel retardation assays, nor by the yeast two hybrid system, clues on the functionality of DnmA could be obtained. However, immunological detection of the methylation mark with an α - 5mC antibody gave initial evidence that the DNA of Dictyostelium was methylated. Furthermore, addition of 5-aza-cytidine as demethylating agent to the Dictyostelium medium and subsequent in vitro incubation of the DNA isolated from these cells with recombinant DnmA showed that the enzyme binds slightly better to this target DNA. In order to investigate further the function of the protein, a gene knock-out for dnmA was generated. The gene was successfully disrupted by homologous recombination, the knock-out strain, however, did not show any obvious phenotype under normal laboratory conditions. To identify specific target sequences for DNA methylation, a microarray analysis was carried out. Setting a threshold of at least 1.5 fold for differences in the strength of gene expression, several such genes in the knock-out strain were chosen for further investigation. Among the up-regulated genes were the ESTs representing the gag and the RT genes respectively of the retrotransposon skipper. In addition Northern blot analysis confirmed the up-regulation of skipper in the DnmA knock-out strain. Bisufite treatment and sequencing of specific DNA stretches from skipper revealed that DnmA is responsible for methylation of mostly asymmetric cytosines. Together with skipper, DIRS-1 retrotransposon was found later also to be methylated but was not present on the microarray. Furthermore, skipper transcription was also up-regulated in strains that had genes disrupted encoding components of the RNA interference pathway. In contrast, DIRS 1 expression was not affected by a loss of DnmA but was strongly increased in the strain that had the RNA directed RNA polymerase gene rrpC disrupted. Strains generated by propagating the usual wild type Ax2 and the DnmA knock-out cells over 16 rounds in development were analyzed for transposon activity. Northern blot analysis revealed activation for skipper expression, but not for DIRS-1. A large number of siRNAs were found to be correspondent to the DIRS-1 sequence, suggesting concerted regulation of DIRS-1 expression by RNAi and DNA methylation. In contrast, no siRNAs corresponding to the standard skipper element were found. The data show that DNA methylation plays a crucial role in epigenetic gene regulation in Dictyostelium and that different, partially overlapping mechanisms control transposon silencing for skipper and DIRS-1. To elucidate the mechanism of targeting the protein to particular genes in the Dictyostelium genome, some more genes which were up-regulated in the DnmA knock-out strain were analyzed by bisulfite sequencing. The chosen genes are involved in the multidrug response in other species, but their function in Dictyostelium is uncertain. Bisulfite data showed that two of these genes were methylated at asymmetrical C-residues in the wild type, but not in DnmA knock-out cells. This suggested that DNA methylation in Dictyostelium is involved not only in transposon regulation but also in transcriptional silencing of specific genes.

Using a Double-pass solar drier for drying of bamboo shoots

Three different drying methods, a forced convection double-pass solar drier (DPSD), typical cabinet type natural convection solar drier (CD) and traditional open-sun drying (OSD) were used for draying of bamboo shoots in central Vietnam. During drying the operational parameters such as drying temperature, relative humidity, air velocity, insolation and water evaporation have been recorded hourly. The mean drying temperatures and relative humidity in the drying chamber were 55.2°C, 23.7%; 47.5°C, 37,6%; 36.2°C, 47.8% in DPSD, CD and OSD, respectively. The mean global radiation during all experimental runs was 670 Wm^−2. The result also shows that fastest drying process was occurred in DPSD where the falling-rate period was achieved after 7 hours, in change to OSD where it took 16 hours. The overall drying efficiency was 23.11%, 15.83% and 9.73% in case of DPSD, CD and OSD, respectively. Although the construction cost of DPSD was significantly higher than in CD, the drying costs per one kilogram of bamboo shoots were by 42.8% lower in case of DPSD as compared to CD. Double-pass solar drier was found to be technically and economically suitable for drying of bamboo shoots under the specific conditions in central Vietnam and in all cases, the use of this drier led to considerable reduction in drying time in comparison to traditional open-sun drying.

Perceiving Illumination Inconsistencies in Scenes

The human visual system is adept at detecting and encoding statistical regularities in its spatio-temporal environment. Here we report an unexpected failure of this ability in the context of perceiving inconsistencies in illumination distributions across a scene. Contrary to predictions from previous studies [Enns and Rensink, 1990; Sun and Perona, 1996a, 1996b, 1997], we find that the visual system displays a remarkable lack of sensitivity to illumination inconsistencies, both in experimental stimuli and in images of real scenes. Our results allow us to draw inferences regarding how the visual system encodes illumination distributions across scenes. Specifically, they suggest that the visual system does not verify the global consistency of locally derived estimates of illumination direction.

Predicting random level and seasonality of hotel prices. A structural equation growth curve approach

This article examines the effect on price of different characteristics of holiday hotels in the sun-and-beach segment, under the hedonic function perspective. Monthly prices of the majority of hotels in the Spanish continental Mediterranean coast are gathered from May to October 1999 from the tour operator catalogues. Hedonic functions are specified as random-effect models and parametrized as structural equation models with two latent variables, a random peak season price and a random width of seasonal fluctuations. Characteristics of the hotel and the region where they are located are used as predictors of both latent variables. Besides hotel category, region, distance to the beach, availability of parking place and room equipment have an effect on peak price and also on seasonality. 3- star hotels have the highest seasonality and hotels located in the southern regions the lowest, which could be explained by a warmer climate in autumn

Validating Co-Training Models for Web Image Classification

Co-training is a semi-supervised learning method that is designed to take advantage of the redundancy that is present when the object to be identified has multiple descriptions. Co-training is known to work well when the multiple descriptions are conditional independent given the class of the object. The presence of multiple descriptions of objects in the form of text, images, audio and video in multimedia applications appears to provide redundancy in the form that may be suitable for co-training. In this paper, we investigate the suitability of utilizing text and image data from the Web for co-training. We perform measurements to find indications of conditional independence in the texts and images obtained from the Web. Our measurements suggest that conditional independence is likely to be present in the data. Our experiments, within a relevance feedback framework to test whether a method that exploits the conditional independence outperforms methods that do not, also indicate that better performance can indeed be obtained by designing algorithms that exploit this form of the redundancy when it is present.

Room-temperature continuous-wave operation of GaInNAs/GaAs quantum dot laser with GaAsN barrier grown by solid source molecular beam epitaxy

We present the results of GaInNAs/GaAs quantum dot structures with GaAsN barrier layers grown by solid source molecular beam epitaxy. Extension of the emission wavelength of GaInNAs quantum dots by ~170nm was observed in samples with GaAsN barriers in place of GaAs. However, optimization of the GaAsN barrier layer thickness is necessary to avoid degradation in luminescence intensity and structural property of the GaInNAs dots. Lasers with GaInNAs quantum dots as active layer were fabricated and room-temperature continuous-wave lasing was observed for the first time. Lasing occurs via the ground state at ~1.2μm, with threshold current density of 2.1kA/cm[superscript 2] and maximum output power of 16mW. These results are significantly better than previously reported values for this quantum-dot system.

A Two-level Prediction Model for Deep Reactive Ion Etch (DRIE)

We contribute a quantitative and systematic model to capture etch non-uniformity in deep reactive ion etch of microelectromechanical systems (MEMS) devices. Deep reactive ion etch is commonly used in MEMS fabrication where high-aspect ratio features are to be produced in silicon. It is typical for many supposedly identical devices, perhaps of diameter 10 mm, to be etched simultaneously into one silicon wafer of diameter 150 mm. Etch non-uniformity depends on uneven distributions of ion and neutral species at the wafer level, and on local consumption of those species at the device, or die, level. An ion–neutral synergism model is constructed from data obtained from etching several layouts of differing pattern opening densities. Such a model is used to predict wafer-level variation with an r.m.s. error below 3%. This model is combined with a die-level model, which we have reported previously, on a MEMS layout. The two-level model is shown to enable prediction of both within-die and wafer-scale etch rate variation for arbitrary wafer loadings.

Surface Functionalization of Monodisperse Magnetic Nanoparticles

We present a systematic methodology to functionalize magnetic nanoparticles through surface-initiated atom-transfer radical polymerization (ATRP). The magnetite nanoparticles are prepared according to the method proposed by Sun et al. (2004), which leads to a monodisperse population of ~ 6 nm particles stabilized by oleic acid. The functionalization of the nanoparticles has been performed by transforming particles into macro-initiators for the ATRP, and to achieve this two different routes have been explored. The first one is the ligand-exchange method, which consists of replacing some oleic acid molecules adsorbed on the particle surface with molecules that act as an initiator for ATRP. The second method consists in using the addition reaction of bromine to the oleic acid double bond, which turns the oleic acid itself into an initiator for the ATRP. We have then grown polymer brushes of a variety of acrylic polymers on the particles, including polyisopropylacrylamide and polyacrylic acid. The nanoparticles so functionalized are water soluble and show responsive behavior: either temperature responsive behavior when polyisopropylacrylamide is grown from the surface or PH responsive in the case of polyacrylic acid. This methodology has potential applications in the control of clustering of magnetic nanoparticles.

Risk Aversion in Inventory Management

Traditional inventory models focus on risk-neutral decision makers, i.e., characterizing replenishment strategies that maximize expected total profit, or equivalently, minimize expected total cost over a planning horizon. In this paper, we propose a framework for incorporating risk aversion in multi-period inventory models as well as multi-period models that coordinate inventory and pricing strategies. In each case, we characterize the optimal policy for various measures of risk that have been commonly used in the finance literature. In particular, we show that the structure of the optimal policy for a decision maker with exponential utility functions is almost identical to the structure of the optimal risk-neutral inventory (and pricing) policies. Computational results demonstrate the importance of this approach not only to risk-averse decision makers, but also to risk-neutral decision makers with limited information on the demand distribution.

Study on Granular Dynamics in Vertically Vibrated Beds using Tracking Technique

The study of granular material is of great interest to many researchers in both engineering and science communities. The importance of such a study derives from its complex rheological character and also its significant role in a wide range of industrial applications, such as coal, food, plastics, pharmaceutical, powder metallurgy and mineral processing. A number of recent reports have been focused on the physics of non-cohesive granular material submitted to vertical vibration in either experimental or theoretical approaches. Such a kind of system can be used to separate, mix and dry granular materials in industries. It exhibits different instability behaviour on its surface when under vertical vibration, for example, avalanching, surface fluidization and surface wave, and these phenomena have attracted particular interest of many researchers. However, its fundamental understanding of the instability mechanism is not yet well-understood. This paper is therefore to study the dynamics of granular motion in such a kind of system using Positron Emission Particle Tracking (PEPT), which allows the motion of a single tracer particle to be followed in a non-invasive way. Features of the solids motion such as cycle frequency and dispersion index were investigated via means of authors’ specially-written programmes. Regardless of the surface behaviour, particles are found to travel in rotational movement in horizontal plane. Particle cycle frequency is found to increase strongly with increasing vibration amplitude. Particle dispersion also increased strongly with vibration amplitude. Horizontal dispersion is observed to always exceed vertical dispersion.

La influencia del utopismo renacentista en la consolidación de la identidad internacional de Hispanoamérica. Estudio de caso : Tomaso de Campanella y la Teología de la Liberación

El descubrimiento de América significó el ensanchamiento de las fronteras mentales que sobre el universo tenían los europeos renacentistas. La existencia de un Nuevo Mundo produjo la necesidad en filósofos y escritores de crear sociedades imaginarias que debían ser implantadas allende el océano como ideales de perfección o utopías. Esta corriente de creadores utópicos que prometían construir una América virtuosa y libre de los vicios de la desgastada Europa, conocido ahora como el Utopismo Renacentista, selló para siempre el destino histórico de la América Hispánica. El Nuevo Mundo sería desde su más temprana colonización el crisol de los anhelos humanos y el origen mismo de las utopías. Fenómenos tales como el caudillismo, el populismo, la Teología de la Liberación, entre otros, profundamente enraizados en el espíritu hispanoamericano, pueden ser también comprendidos a partir del carácter utópico del continente, y por tanto, el utopismo se convierte en rasgo fundamental de la identidad internacional de Hispanoamérica. El caso de la Teología de la Liberación es analizado a la luz de la obra del filósofo italiano Tomaso de Campanella, La Ciudad del Sol, donde se encuentra que aspectos como el comunitarismo, la religión como fuente de lo político y el establecimiento de ideales de perfección social son parte fundamental de la esencia identitaria de la América Española.

A Motion compensated filtering approach to remove sunlight flicker in shallow water images

A common problem in video surveys in very shallow waters is the presence of strong light fluctuations, due to sun light refraction. Refracted sunlight casts fast moving patterns, which can significantly degrade the quality of the acquired data. Motivated by the growing need to improve the quality of shallow water imagery, we propose a method to remove sunlight patterns in video sequences. The method exploits the fact that video sequences allow several observations of the same area of the sea floor, over time. It is based on computing the image difference between a given reference frame and the temporal median of a registered set of neighboring images. A key observation is that this difference will have two components with separable spectral content. One is related to the illumination field (lower spatial frequencies) and the other to the registration error (higher frequencies). The illumination field, recovered by lowpass filtering, is used to correct the reference image. In addition to removing the sunflickering patterns, an important advantage of the approach is the ability to preserve the sharpness in corrected image, even in the presence of registration inaccuracies. The effectiveness of the method is illustrated in image sets acquired under strong camera motion containing non-rigid benthic structures. The results testify the good performance and generality of the approach