Manufacture of DPFC-DMS polymer in the SKG range

BPFC-DMS block copolymers were synthesized on a pre-pilot scale (i.e., to 5 Kg lots) and subsequently fabricated into clear, colorless films. Details of the synthesis procedures, property determinations, and film casting techniques are presented. Solubility, viscosity and molecular weight characteristics of the resulting product are reported

Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping

We have mapped sequence-directed nucleosome positioning on genomic DNA molecules using high-throughput sequencing. Chromatins, prepared by reconstitution with either chicken or frog histones, were separately digested to mononucleosomes using either micrococcal nuclease (MNase) or caspase-activated DNase (CAD). Both enzymes preferentially cleave internucleosomal (linker) DNA, although they do so by markedly different mechanisms. MNase has hitherto been very widely used to map nucleosomes, although concerns have been raised over its potential to introduce bias. Having identified the locations and quantified the strength of both the chicken or frog histone octamer binding sites on each DNA, the results obtained with the two enzymes were compared using a variety of criteria. Both enzymes displayed sequence specificity in their preferred cleavage sites, although the nature of this selectivity was distinct for the two enzymes. In addition, nucleosomes produced by CAD nuclease are 8–10 bp longer than those produced with MNase, with the CAD cleavage sites tending to be 4–5 bp further out from the nucleosomal dyad than the corresponding MNase cleavage sites. Despite these notable differences in cleavage behaviour, the two nucleases identified essentially equivalent patterns of nucleosome positioning sites on each of the DNAs tested, an observation that was independent of the histone type. These results indicate that biases in nucleosome positioning data collected using MNase are, under our conditions, not significant

Restoring riparian ecosystems: The challenge of accommodating variability and designing restoration trajectories

Flood disturbance processes play a key role in the functioning of riparian ecosystems and in the maintenance of biodiversity along river corridors. As a result, riparian ecosystems can be described as mobile habitat mosaics characterized by variability and unpredictability. Any river restoration initiative should aim to mimic these attributes. This paper suggests that there needs to be an increased institutional capacity to accept some levels of both variability and unpredictability in the ecological outcomes of river restoration projects. Restoration projects have frequently used some form of historical or contemporary reference system to define objectives and to help in the evaluation process. Using these reference systems can give a false sense of the predictability of ecological outcomes. We suggest that reference systems need to be used with caution for six reasons: (1) there are often no appropriate reference systems to use, (2) many catchment parameters have changed since the times of chosen historic reference systems, (3) climate change has been continuous throughout the Holocene, (4) projected climate change is of uncertain magnitude, (5) alien species cannot be avoided, and (6) landscape context changes through time. As well as defining short-term objectives, we suggest that river restoration projects should also formulate longer-term (decadel) restoration trajectories that are less predictable but more representative of real system attributes. Restoration trajectories could be defined using a range of ecological outcomes to accommodate interannual variability. The challenges of defining what levels of variability are important for restoring European floodplain forests are used to demonstrate the difficulties of broadening approaches and creating trajectories. In particular, the changing significance of variability at different spatial and temporal scales is discussed. An account is given of a restoration project at Wicken Fen in the United Kingdom in which nondeterministic approaches to goal setting have been initiated

Isolation of Unknown Genes from Human Bone Marrow by Differental Screening and Single-Pass cDNA Sequences Determination

A cDNA sequencing project was initiated to characterize gene expression in human bone marrow and develop strategies to isolate novel genes. Forty-eight random cDNAs from total human bone marrow were subjected to single-pass DNA sequence analysis to determine a limited complexity of mRNAs expressed in the bone marrow. Overall, 8 cDNAs (17%) showed no similarity to known sequences. Information from DNA sequence analysis was used to develop a differential prescreen to subtract unwanted cDNAs and to enrich for unknown cDNAs. Forty-eight cDNAs that were negative with a complex probe were subject to single-pass DNA sequence determination. Of these prescreened cDNAs, the number of unknown sequences increased to 23 (48%). Unknown cDNAs were also characterized by RNA expression analysis using 25 different human leukemic cell lines. Of 13 unknown cDNAs tested, 10 were expressed in all cell types tested and 3 revealed a hematopoietic lineage-restricted expression pattern. Interestingly, while a total of only 96 bone marrow cDNAs were sequenced, 31 of these cDNAs represent sequences from unknown genes and 12 showed significant similarities to sequences in the data bases. One cDNA revealed a significant similarity to a serine/threonine-protein kinase at the amino acid level (56% identity for 123 amino acids) and may represent a previously unknown kinase. Differential screening techniques coupled with single-pass cDNA sequence analysis may prove to be a powerful and simple technique to examine developmental gene expression

Identification of multiple distinct Snf2 subfamilies with conserved structural motifs

The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function

Quasars in the MAMBO blank field survey

Our MAMBO 1.2 mm blank field imaging survey of ~0.75 sqd has uncovered four unusually bright sources, with flux densities between 10 and 90 mJy, all located in the Abell 2125 field. The three brightest are flat spectrum radio sources with bright optical and X-ray counterparts. Their mm and radio flux densities are variable on timescales of months. Their X-ray luminosities classify them as quasars. The faintest of the four mm bright sources appears to be a bright, radio-quiet starburst at z~3, similar to the sources seen at lower flux densities in the MAMBO and SCUBA surveys. It may also host a mildly obscured AGN of quasar-like X-ray luminosity. The three non-thermal mm sources imply an areal density of flat spectrum radio sources higher by at least 7 compared with that expected from an extrapolation of the lower frequency radio number counts.Comment: 8 pages, 7 figures. Accepted for publication by A&

Modelling multi-protein complexes using PELDOR distance measurements for rigid body minimisation experiments using XPLOR-NIH

Crystallographic and NMR approaches have provided a wealth of structural information about protein domains. However, often these domains are found as components of larger multi domain polypeptides or complexes. Orienting domains within such contexts can provide powerful new insight into their function. The combination of site specific spin labelling and Pulsed Electron Double Resonance (PELDOR) provide a means of obtaining structural measurements that can be used to generate models describing how such domains are oriented. Here we describe a pipeline for modelling the location of thio-reactive nitroxyl spin locations to engineered sties on the histone chaperone Vps75. We then use a combination of experimentally determined measurements and symmetry constraints to model the orientation in which homodimers of Vps75 associate to form homotetramers using the XPLOR-NIH platform. This provides a working example of how PELDOR measurements can be used to generate a structural model

XMMU J0541.8-6659, a new supernova remnant in the Large Magellanic Cloud

The high sensitivity of the XMM-Newton instrumentation offers the opportunity to study faint and extended sources in the Milky Way and nearby galaxies such as the Large Magellanic Cloud (LMC) in detail. The ROSAT PSPC survey of the LMC has revealed more than 700 X-ray sources, among which there are 46 supernova remnants (SNRs) and candidates. We have observed the field around one of the most promising SNR candidates in the ROSAT PSPC catalogue, labelled [HP99] 456 with XMM-Newton, to determine its nature. We investigated the XMM-Newton data along with new radio-continuum, near infrared and optical data. In particular, spectral and morphological studies of the X-ray and radio data were performed. The X-ray images obtained in different energy bands reveal two different structures. Below 1.0 keV the X-ray emission shows the shell-like morphology of an SNR with a diameter of ~73 pc, one of the largest known in the LMC. For its thermal spectrum we estimate an electron temperature of (0.49 +/- 0.12)keV assuming non-equilibrium ionisation. The X-ray images above 1.0 keV reveal a less extended source within the SNR emission, located ~1' west of the centre of the SNR and coincident with bright point sources detected in radio-continuum. This hard component has an extent of 0.9' (i.e. ~13 pc at a distance of ~50 kpc) and a non-thermal spectrum. The hard source coincides in position with the ROSAT source [HP99] 456 and shows an indication for substructure. We firmly identify a new SNR in the LMC with a shell-like morphology and a thermal spectrum. Assuming the SNR to be in the Sedov phase yields an age of ~23 kyr. We explore possible associations of the hard non-thermal emitting component with a pulsar wind nebula (PWN) or background active galactic nuclei (AGN).Comment: 8 pages, 7 figures, accepted for publication in Astronomy and Astrophysic