X-linked mental retardation and epigenetics

The search for the genetic defects in constitutional diseases has so far been restricted to direct methods for the identification of genetic mutations in the patients' genome. Traditional methods such as karyotyping, FISH, mutation screening, positional cloning and CGH, have been complemented with newer methods including array-CGH and PCR-based approaches (MLPA, qPCR). These methods have revealed a high number of genetic or genomic aberrations that result in an altered expression or reduced functional activity of key proteins. For a significant percentage of patients with congenital disease however, the underlying cause has not been resolved strongly suggesting that yet other mechanisms could play important roles in their etiology. Alterations of the 'native' epigenetic imprint might constitute such a novel mechanism. Epigenetics, heritable changes that do not rely on the nucleotide sequence, has already been shown to play a determining role in embryonic development, X-inactivation, and cell differentiation in mammals. Recent progress in the development of techniques to study these processes on full genome scale has stimulated researchers to investigate the role of epigenetic modifications in cancer as well as in constitutional diseases. We will focus on mental impairment because of the growing evidence for the contribution of epigenetics in memory formation and cognition. Disturbance of the epigenetic profile due to direct alterations at genomic regions, or failure of the epigenetic machinery due to genetic mutations in one of its components, has been demonstrated in cognitive derangements in a number of neurological disorders now. It is therefore tempting to speculate that the cognitive deficit in a significant percentage of patients with unexplained mental retardation results from epigenetic modifications.     

And then there were acyl coenzyme A:cholesterol acyl transferase inhibitors

PURPOSE OF REVIEW: The reputation of acyl coenzyme A:cholesterol acyltransferase (ACAT) inhibitors has changed profoundly from promising new drugs for cardiovascular prevention to drugs without clinical benefits or possibly even with adverse effects. RECENT FINDINGS: ACAT inhibitors decrease the intracellular conversion of free cholesterol into cholesteryl ester in a number of tissues, including intestine, liver and macrophages. In contrast to promising results in experimental animal models, all subsequent clinical studies in humans with ACAT inhibitors failed to show lipid profile changes as well as reductions in surrogate markers for coronary artery disease. In fact, there was even a tendency towards an increase in atheroma burden in the most recent and well executed clinical trials. In addition, the inhibition of this pivotal enzyme in cholesterol esterification may interfere with reverse cholesterol transport. SUMMARY: In our opinion, the consistent negative findings in recent clinical trials have virtually eliminated the chances for this class of drugs to be introduced for cardiovascular prevention. Possible strategies focused on selective ACAT 2 inhibition or the combination of ACAT inhibitors with compounds that stimulate reverse cholesterol transport may prove to have clinical benefit. This will have to await further clinical research in humans, however, as, obviously, rodent models cannot provide reliable data as to the efficacy of this class of drugs in humans.     

DNA methylation and normal chromosome behavior in Neurospora depend on five components of a histone methyltransferase complex, DCDC

Methylation of DNA and of Lysine 9 on histone H3 (H3K9) is associated with gene silencing in many animals, plants, and fungi. In Neurospora crassa, methylation of H3K9 by DIM-5 directs cytosine methylation by recruiting a complex containing Heterochromatin Protein-1 (HP1) and the DIM-2 DNA methyltransferase. We report genetic, proteomic, and biochemical investigations into how DIM-5 is controlled. These studies revealed DCDC, a previously unknown protein complex including DIM-5, DIM-7, DIM-9, CUL4, and DDB1. Components of DCDC are required for H3K9me3, proper chromosome segregation, and DNA methylation. DCDC-defective strains, but not HP1-defective strains, are hypersensitive to MMS, revealing an HP1-independent function of H3K9 methylation. In addition to DDB1, DIM-7, and the WD40 domain protein DIM-9, other presumptive DCAFs (DDB1/CUL4 associated factors) co-purified with CUL4, suggesting that CUL4/DDB1 forms multiple complexes with distinct functions. This conclusion was supported by results of drug sensitivity tests. CUL4, DDB1, and DIM-9 are not required for localization of DIM-5 to incipient heterochromatin domains, indicating that recruitment of DIM-5 to chromatin is not sufficient to direct H3K9me3. DIM-7 is required for DIM-5 localization and mediates interaction of DIM-5 with DDB1/CUL4 through DIM-9. These data support a two-step mechanism for H3K9 methylation in Neurospora.     

Applying double-magnetic induction to measure head-unrestrained gaze shifts: calibration and validation in monkey

The double magnetic induction (DMI) method has successfully been used to record head-unrestrained gaze shifts in human subjects (Bremen et?al., J Neurosci Methods 160:75-84, 2007a, J Neurophysiol, 98:3759-3769, 2007b). This method employs a small golden ring placed on the eye that, when positioned within oscillating magnetic fields, induces orientation-dependent voltages in a pickup coil in front of the eye. Here we develop and test a streamlined calibration routine for use with experimental animals, in particular, with monkeys. The calibration routine requires the animal solely to accurately follow visual targets presented at random locations in the visual field. Animals can readily learn this task. In addition, we use the fact that the pickup coil can be fixed rigidly and reproducibly on implants on the animal's skull. Therefore, accumulation of calibration data leads to increasing accuracy. As a first step, we simulated gaze shifts and the resulting DMI signals. Our simulations showed that the complex DMI signals can be effectively calibrated with the use of random target sequences, which elicit substantial decoupling of eye- and head orientations in a natural way. Subsequently, we tested our paradigm on three macaque monkeys. Our results show that the data for a successful calibration can be collected in a single recording session, in which the monkey makes about 1,500-2,000 goal-directed saccades. We obtained a resolution of 30 arc minutes (measurement range [-60,+60]°). This resolution compares to the fixation resolution of the monkey's oculomotor system, and to the standard scleral search-coil method.     

Towards a mechanistic understanding of the impacts of nitrogen deposition on producer–consumer interactions

Nitrogen (N) deposition has increased substantially since the second half of the 20th century due to human activities. This increase of reactive N into the biosphere has major implications for ecosystem functioning, including primary production, soil and water chemistry and producer community structure and diversity. Increased N deposition is also linked to the decline of insects observed over recent decades. However, we currently lack a mechanistic understanding of the effects of high N deposition on individual fitness, species richness and community structure of both invertebrate and vertebrate consumers. Here, we review the effects of N deposition on producer–consumer interactions, focusing on five existing ecological frameworks: C:N:P ecological stoichiometry, trace element ecological stoichiometry, nutritional geometry, essential micronutrients and allelochemicals. We link reported N deposition-mediated changes in producer quality to life-history strategies and traits of consumers, to gain a mechanistic understanding of the direction of response in consumers. We conclude that high N deposition influences producer quality via eutrophication and acidification pathways. This makes oligotrophic poorly buffered ecosystems most vulnerable to significant changes in producer quality. Changes in producer quality between the reviewed frameworks are often interlinked, complicating predictions of the effects of high N deposition on producer quality. The degree and direction of fitness responses of consumers to changes in producer quality varies among species but can be explained by differences in life-history traits and strategies, particularly those affecting species nutrient intake regulation, mobility, relative growth rate, host-plant specialisation, ontogeny and physiology. To increase our understanding of the effects of N deposition on these complex mechanisms, the inclusion of life-history traits of consumer species in future study designs is pivotal. Based on the reviewed literature, we formulate five hypotheses on the mechanisms underlying the effects of high N deposition on consumers, by linking effects of nutritional ecological frameworks to life-history strategies. Importantly, we expect that N-deposition-mediated changes in producer quality will result in a net decrease in consumer community as well as functional diversity. Moreover, we anticipate an increased risk of outbreak events of a small subset of generalist species, with concomitant declines in a multitude of specialist species. Overall, linking ecological frameworks with consumer life-history strategies provides a mechanistic understanding of the impacts of high N deposition on producer–consumer interactions, which can inform management towards more effective mitigation strategies.     

Comparing the Quality of Crowdsourced Data Contributed by Expert and Non-Experts

There is currently a lack of in-situ environmental data for the calibration and validation of remotely sensed products and for the development and verification of models. Crowdsourcing is increasingly being seen as one potentially powerful way of increasing the supply of in-situ data but there are a number of concerns over the subsequent use of the data, in particular over data quality. This paper examined crowdsourced data from the Geo-Wiki crowdsourcing tool for land cover validation to determine whether there were significant differences in quality between the answers provided by experts and non-experts in the domain of remote sensing and therefore the extent to which crowdsourced data describing human impact and land cover can be used in further scientific research. The results showed that there was little difference between experts and non-experts in identifying human impact although results varied by land cover while experts were better than non-experts in identifying the land cover type. This suggests the need to create training materials with more examples in those areas where difficulties in identification were encountered, and to offer some method for contributors to reflect on the information they contribute, perhaps by feeding back the evaluations of their contributed data or by making additional training materials available. Accuracies were also found to be higher when the volunteers were more consistent in their responses at a given location and when they indicated higher confidence, which suggests that these additional pieces of information could be used in the development of robust measures of quality in the future.     

Ubiquitin Ligase HUWE1 Regulates Axon Branching through the Wnt/β-Catenin Pathway in a Drosophila Model for Intellectual Disability

We recently reported that duplication of the E3 ubiquitin ligase HUWE1 results in intellectual disability (ID) in male patients. However, the underlying molecular mechanism remains unknown. We used Drosophila melanogaster as a model to investigate the effect of increased HUWE1 levels on the developing nervous system. Similar to the observed levels in patients we overexpressed the HUWE1 mRNA about 2-fold in the fly. The development of the mushroom body and neuromuscular junctions were not altered, and basal neurotransmission was unaffected. These data are in agreement with normal learning and memory in the courtship conditioning paradigm. However, a disturbed branching phenotype at the axon terminals of the dorsal cluster neurons (DCN) was detected. Interestingly, overexpression of HUWE1 was found to decrease the protein levels of dishevelled (dsh) by 50%. As dsh as well as Fz2 mutant flies showed the same disturbed DCN branching phenotype, and the constitutive active homolog of β-catenin, armadillo, could partially rescue this phenotype, our data strongly suggest that increased dosage of HUWE1 compromises the Wnt/β-catenin pathway possibly by enhancing the degradation of dsh.     

Imaging Dendritic Spines of Rat Primary Hippocampal Neurons using Structured Illumination Microscopy

Dendritic spines are protrusions emerging from the dendrite of a neuron and represent the primary postsynaptic targets of excitatory inputs in the brain. Technological advances have identified these structures as key elements in neuron connectivity and synaptic plasticity. The quantitative analysis of spine morphology using light microscopy remains an essential problem due to technical limitations associated with light''s intrinsic refraction limit. Dendritic spines can be readily identified by confocal laser-scanning fluorescence microscopy. However, measuring subtle changes in the shape and size of spines is difficult because spine dimensions other than length are usually smaller than conventional optical resolution fixed by light microscopy''s theoretical resolution limit of 200 nm.Several recently developed super resolution techniques have been used to image cellular structures smaller than the 200 nm, including dendritic spines. These techniques are based on classical far-field operations and therefore allow the use of existing sample preparation methods and to image beyond the surface of a specimen. Described here is a working protocol to apply super resolution structured illumination microscopy (SIM) to the imaging of dendritic spines in primary hippocampal neuron cultures. Possible applications of SIM overlap with those of confocal microscopy. However, the two techniques present different applicability. SIM offers higher effective lateral resolution, while confocal microscopy, due to the usage of a physical pinhole, achieves resolution improvement at the expense of removal of out of focus light. In this protocol, primary neurons are cultured on glass coverslips using a standard protocol, transfected with DNA plasmids encoding fluorescent proteins and imaged using SIM. The whole protocol described herein takes approximately 2 weeks, because dendritic spines are imaged after 16-17 days in vitro, when dendritic development is optimal. After completion of the protocol, dendritic spines can be reconstructed in 3D from series of SIM image stacks using specialized software.     

Functional finishing of aminated polyester using biopolymer-based polyelectrolyte microgels

This study focuses on a microgel-based functionalization method applicable to polyester textiles for improving their hydrophilicity and/or moisture-management properties, eventually enhancing wear comfort. The method proposed aims at achieving pH-/temperature-controlled wettability of polyester within a physiological pH/temperature range. First, primary amine groups are created on polyester surfaces using ethylenediamine; second, biopolymer-based polyelectrolyte microgels are incorporated using the natural cross-linker genipin. The microgels consist of the pH-responsive natural polysaccharide chitosan and pH/thermoresponsive poly(N-isopropylacrylamide-co-acrylic acid) microparticles. Scanning electron microscopy confirmed the microgel presence on polyester surfaces. X-ray photoelectron spectroscopy revealed nitrogen concentration, supporting increased microscopy results. Electrokinetic analysis showed that functionalized polyester surfaces have a zero-charge point at pH 6.5, close to the microgel isoelectric point. Dynamic wetting measurements revealed that functionalized polyester has shorter total water absorption time than the reference. This absorption time is also pH dependent, based on dynamic contact angle and micro-roughness measurements, which indicated microgel swelling at different pH values. Furthermore, at 40 °C functionalized polyester has higher vapor transmission rates than the reference, even at high relative humidity. This was attributed to the microgel thermoresponsiveness, which was confirmed through the almost 50% decrease in microparticle size between 20 and 40 °C, as determined by dynamic light scattering measurements.