Chromatin state changes during neural development revealed by in vivo cell-type specific profiling.

A key question in developmental biology is how cellular differentiation is controlled during development. While transitions between trithorax-group (TrxG) and polycomb-group (PcG) chromatin states are vital for the differentiation of ES cells to multipotent stem cells, little is known regarding the role of chromatin states during development of the brain. Here we show that large-scale chromatin remodelling occurs during Drosophila neural development. We demonstrate that the majority of genes activated during neuronal differentiation are silent in neural stem cells (NSCs) and occupy black chromatin and a TrxG-repressive state. In neurons, almost all key NSC genes are switched off via HP1-mediated repression. PcG-mediated repression does not play a significant role in regulating these genes, but instead regulates lineage-specific transcription factors that control spatial and temporal patterning in the brain. Combined, our data suggest that forms of chromatin other than canonical PcG/TrxG transitions take over key roles during neural development

damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.

UNLABELLED: DamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with normalization based on read-counts alone can lead to high background and the loss of bound signal. DamID-seq thus presents novel challenges in terms of normalization and background minimization. We describe here damidseq_pipeline, a software pipeline that performs automatic normalization and background reduction on multiple DamID-seq FASTQ datasets. AVAILABILITY AND IMPLEMENTATION: Open-source and freely available from http://owenjm.github.io/damidseq_pipeline. The damidseq_pipeline is implemented in Perl and is compatible with any Unix-based operating system (e.g. Linux, Mac OSX). CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.We thank Charles Bradshaw for helpful comments on the software. This work was supported by the BBSRC [BB/L00786X/1] and Wellcome Trust [092545]. The Gurdon Institute is supported by core funding from the Wellcome Trust [092096] and CRUK [C6946/A14492].This is the final published version. It first appeared at http://dx.doi.org/10.1093/bioinformatics/btv38

Three-dimensional localization of CENP-A suggests a complex higher order structure of centromeric chromatin

The histone H3 variant centromere protein A (CENP-A) is central to centromere formation throughout eukaryotes. A long-standing question in centromere biology has been the organization of CENP-A at the centromere and its implications for the structure of centromeric chromatin. In this study, we describe the three-dimensional localization of CENP-A at the inner kinetochore plate through serial-section transmission electron microscopy of human mitotic chromosomes. At the kinetochores of normal centromeres and at a neocentromere, CENP-A occupies a compact domain at the inner kinetochore plate, stretching across two thirds of the length of the constriction but encompassing only one third of the constriction width and height. Within this domain, evidence of substructure is apparent. Combined with previous chromatin immunoprecipitation results (Saffery, R., H. Sumer, S. Hassan, L.H. Wong, J.M. Craig, K. Todokoro, M. Anderson, A. Stafford, and K.H.A. Choo. 2003. Mol. Cell. 12:509–516; Chueh, A.C., L.H. Wong, N. Wong, and K.H.A. Choo. 2005. Hum. Mol. Genet. 14:85–93), our data suggest that centromeric chromatin is arranged in a coiled 30-nm fiber that is itself coiled or folded to form a higher order structure

On the shape of barchan dunes

Barchans are crescent-shaped sand dunes forming in aride regions with unidirectional wind and limited sand supply. We report analytical and numerical results for dune shapes under different environmental conditions as obtained from the so-called `minimal model' of aeolian sand dunes. The profiles of longitudinal vertical slices (i.e. along the wind direction) are analyzed as a function of wind speed and sand supply. Shape transitions can be induced by changes of mass, wind speed and sand supply. Within a minimal extension of the model to the transverse direction the scale-invariant profile of transverse vertical cuts can be derived analytically.Comment: to appear in J. Phys.: Condens. Matter 17 (2005

Structural Basis for α-Conotoxin Potency and Selectivity

Parkinson\u27s disease is a debilitating movement disorder characterized by altered levels of α6β2* nicotinic acetylcholine receptors (nAChRs) localized on presynaptic striatal catecholaminergic neurons. α-Conotoxin MII (α-CTx MII) is a highly useful ligand to probe α6ß2 nAChRs structure and function, but it does not discriminate among closely related α6* nAChR subtypes. Modification of the α-CTx MII primary sequence led to the identification of α-CTx MII[E11A], an analog with 500-5300 fold discrimination between α6* subtypes found in both human and non-human primates. α-CTx MII[E11A] binds most strongly (femtomolar dissociation constant) to the high affinity α6* nAChR, a subtype that is selectively lost in Parkinson\u27s disease. Here we present the three-dimensional solution structure for α-CTx MII[E11A] as determined by two-dimensional 1H NMR spectroscopy to 0.13 +/- 0.09 Ǻ backbone and 0.45 +/- 0.08 Ǻ heavy atom root mean square deviation from mean structure. Structural comparisons suggest that the increased hydrophobic area of α-CTx MII[E11A] relative to other members of the α-CTx family may be responsible for its exceptionally high affinity for α6α4β2* nAChR as well as discrimination between α6ß2 and α3β2 containing nAChRs. This finding may enable the rational design of novel peptide analogs that demonstrate enhanced specificity for α6* nAChR subunit interfaces and provide a means to better understand nAChR structural determinants that modulate brain dopamine levels and the pathophysiology of Parkinson\u27s disease

Differential rotation of nonlinear r-modes

Differential rotation of r-modes is investigated within the nonlinear theory up to second order in the mode amplitude in the case of a slowly-rotating, Newtonian, barotropic, perfect-fluid star. We find a nonlinear extension of the linear r-mode, which represents differential rotation that produces large scale drifts of fluid elements along stellar latitudes. This solution includes a piece induced by first-order quantities and another one which is a pure second-order effect. Since the latter is stratified on cylinders, it cannot cancel differential rotation induced by first-order quantities, which is not stratified on cylinders. It is shown that, unlikely the situation in the linearized theory, r-modes do not preserve vorticity of fluid elements at second-order. It is also shown that the physical angular momentum and energy of the perturbation are, in general, different from the corresponding canonical quantities.Comment: 9 pages, revtex4; section III revised, comments added in Introduction and Conclusions, references updated; to appear in Phys. Rev.

HST optical spectral index map of the jet of 3C 273

We present HST images at 622 nm and 300 nm of the jet in 3C273 and determine the run of the optical spectral index at 0.2" along the jet. The smoothness of spectral index changes shows that the physical conditions are varying smoothly across the jet. There is no correlation between the optical flux and spectral index, as would be expected for relativistic electrons suffering strong cooling due to synchrotron emission. We find no evidence for localized acceleration or loss sites. This suggests that the spectral shape is not changing much throughout the jet. We show that relativistic beaming and/or sub-equipartition magnetic fields cannot remove the discrepancy between light-travel time along the jet and the lifetime of electrons emitting optical synchrotron radiation. We consider this further evidence in favour of a distributed electron acceleration process.Comment: Accepted for publication by Astronomy and Astrophysics (13 pages, 8 figures

Land cover and nutrient enrichment regulates low-molecular weight dissolved organic matter turnover in freshwater ecosystems

Dissolved organic matter (DOM) is a complex mixture of carbon-containing compounds. The low-molecular weight (LMW) fraction constitutes thousands of different compounds and represents a substantial proportion of DOM in aquatic ecosystems. The turnover rates of this LMW DOM can be extremely high. Due to the challenges of measuring this pool at a molecular scale, comparatively little is known of the fate of LMW DOM compounds in lotic systems. This study addresses this knowledge gap, investigating the microbial processing of LMW DOM across 45 sites representing a range of physicochemical gradients and dominant land covers in the United Kingdom. Radioisotope tracers representing LMW dissolved organic carbon (DOC) (glucose), dissolved organic nitrogen (DON) (amino acid mixture), dissolved organic phosphorus (DOP) (glucose-6-phosphate), and soluble reactive phosphorus (SRP, measured as orthophosphate) were used to measure the microbial uptake of different DOM compounds in river waters. The amount of DOM biodegradation varied between different components (DON ≥ DOC > DOP), with the rate of turnover of all three increasing along a gradient of N and P enrichment across the range of sites. Conversely, the uptake of SRP decreased along this same gradient. This was ascribed to preferential utilization of DOP over SRP. Dominant land cover had a significant effect on DOM use as a resource, due to its control of nutrient enrichment within the catchments. We conclude that nutrient enrichment of river waters will lead to further DOM removal from the water column, increased microbial growth, and a decrease in stream oxygen saturation, exacerbating the effects of eutrophication in rivers