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Diffractive Fresnel zone plates made of tungsten show great promise for focusing hard x-ray free-electron laser (XFEL) radiation to very small spot sizes. However, they have to withstand the high-intensity pulses of the beam without being damaged. This might be problematic since each XFEL pulse will create a significant temperature increase in the zone plate nanostructures and it is therefore crucial that the optics are thermally stable, even for a large number of pulses. Here we have studied the thermal stability of tungsten zone-plate- like nanostructures on diamond substrates using a pulsed Nd:YAG laser which creates temperature profiles similar to those expected from XFEL pulses. We found that the structures remained intact up to a laser fluence of 100mJcm 2 , corresponding to a 6keV x-ray fluence of 590mJcm 2 , which is above typical fluence levels in an unfocused XFEL beam. We have also performed an initial damage experiment at the LCLS hard XFEL facility at SLAC National Accelerator Laboratory, where a tungsten zone plate on a diamond substrate was exposed to 10 5 pulses of 6keV x-rays with a pulse fluence of 350mJcm 2 without any damage occurring.

The authors report on a new tungsten-hardmask-based diamond dry-etch process for fabricating diamond zone plate lenses with a high aspect ratio. The tungsten hardmask is structured by electron-beam lithography, together with Cl2/O2 and SF6/O2 reactive ion etching in a trilayer resist-chromium-tungsten stack. The underlying diamond is then etched in an O2 plasma. The authors demonstrate excellent-quality diamond gratings with half-pitch down to 80 nm and a height of 2.6 μm, as well as zone plates with a 75 μm diameter and 100 nm outermost zone width. The diffraction efficiency of the zone plates is measured to 14.5% at an 8 keV x-ray energy, and the imaging properties were investigated in a scanning microscope arrangement showing sub-100-nm resolution. The imaging and thermal properties of these lenses make them suitable for use with high-brightness x-ray free-electron laser sources.

Among the many strategies employed by parasites for immune evasion and host manipulation, one of the most fascinating is molecular mimicry. With genome sequences available for host and parasite, mimicry of linear amino acid epitopes can be investigated by comparative genomics. Here we developed an in silico pipeline for genome-wide identification of molecular mimicry candidate proteins or epitopes. The predicted proteome of a given parasite was broken down into overlapping fragments, each of which was screened for close hits in the human proteome. Control searches were carried out against unrelated, free-living eukaryotes to eliminate the generally conserved proteins, and with randomized versions of the parasite proteins to get an estimate of statistical significance. This simple but computation-intensive approach yielded interesting candidates from human-pathogenic parasites. From Plasmodium falciparum, it returned a 14 amino acid motif in several of the PfEMP1 variants identical to part of the heparin-binding domain in the immunosuppressive serum protein vitronectin. And in Brugia malayi, fragments were detected that matched to periphilin-1, a protein of cell-cell junctions involved in barrier formation. All the results are publicly available by means of mimicDB, a searchable online database for molecular mimicry candidates from pathogens. To our knowledge, this is the first genome-wide survey for molecular mimicry proteins in parasites. The strategy can be adopted to any pair of host and pathogen, once appropriate negative control organisms are chosen. MimicDB provides a host of new starting points to gain insights into the molecular nature of host-pathogen interactions.

The pathway for RNA interference is widespread in metazoans and participates in numerous cellular tasks, from gene silencing to chromatin remodeling and protection against retrotransposition. The unicellular eukaryote Trypanosoma cruzi is missing the canonical RNAi pathway and is unable to induce RNAi-related processes. To further understand alternative RNA pathways operating in this organism, we have performed deep sequencing and genome-wide analyses of a size-fractioned cDNA library (16–61 nt) from the epimastigote life stage. Deep sequencing generated 582,243 short sequences of which 91% could be aligned with the genome sequence. About 95–98% of the aligned data (depending on the haplotype) corresponded to small RNAs derived from tRNAs, rRNAs, snRNAs and snoRNAs. The largest class consisted of tRNA-derived small RNAs which primarily originated from the 3′ end of tRNAs, followed by small RNAs derived from rRNA. The remaining sequences revealed the presence of 92 novel transcribed loci, of which 79 did not show homology to known RNA classes., Author Summary Chagas' disease is a major health problem in Latin America and is caused by the protozoan parasite Trypanosoma cruzi. T. cruzi lacks the pathway for RNA interference, which is widespread among eukaryotes, and is therefore unable to induce RNAi-related processes. In many organisms, small RNAs play an important role in regulating gene expression and other cellular processes. In order to understand if other small RNA pathways are operating in this organism, we performed high throughput sequencing and genome-wide analyses of the short transcriptome. We identified an abundance of small RNAs derived from non-coding RNA genes, including transfer RNAs, ribosomal RNAs as well as small nucleolar RNAs and small nuclear RNAs. Certain tRNA types were overrepresented as precursors for small RNAs. Further, we identified 79 novel small non-coding RNAs, not previously reported. We did not identify canonical small RNAs, like microRNAs and small interfering RNAs, and concluded that these do not exist in T. cruzi. This study has provided insights into the short transcriptome of a major human pathogen and provided starting points for further functional investigation of small RNAs and their biological roles.

The recently launched veterinary anthelmintic drench for sheep (Novartis Animal Health Inc., Switzerland) containing the nematocide monepantel represents a new class of anthelmintics: the amino-acetonitrile derivatives (AADs), much needed in view of widespread resistance to the classical drugs. Recently, it was shown that the ACR-23 protein in Caenorhabditis elegans and a homologous protein, MPTL-1 in Haemonchus contortus, are potential targets for AAD action. Both proteins belong to the DEG-3 subfamily of acetylcholine receptors, which are thought to be nematode-specific, and different from those targeted by the imidazothiazoles (e.g. levamisole). Here we provide further evidence that Cel-ACR-23 and Hco-MPTL-1-like subunits are involved in the monepantel-sensitive phenotype. We performed comparative genomics of ligand-gated ion channel genes from several nematodes and subsequently assessed their sensitivity to anthelmintics. The nematode species in the Caenorhabditis genus, equipped with ACR-23/MPTL-1-like receptor subunits, are sensitive to monepantel (EC5043 µM). Genome sequence information has long been used to identify putative targets for therapeutic intervention. We show how comparative genomics can be applied to predict drug sensitivity when molecular targets of a compound are known or suspected., Author Summary Increased use of anthelmintics has contributed to the emergence of drug-resistant nematodes, causing serious problems for more than one billion sheep worldwide. The last class of compounds indicated for livestock was introduced 28 years ago. Recently, however, Novartis AH developed a new anthelmintic active against drug-resistant nematodes of sheep, the amino-acetonitrile derivative (AAD) monepantel. We have previously indirectly shown that the AADs have a novel mode of action involving acetylcholine receptor subunits: the ACR-23 protein in Caenorhabditis elegans and a homologous protein, MPTL-1 in Haemonchus contortus. To better understand the mode of action of the AADs, we performed comparative genomics of all ligand-gated ion channel genes from a range of organisms, including members from all nematode clades. We confirmed that MPTL-1 belongs to a unique, nematode-specific sub-family of receptor subunits. We also found that some nematode species lack ACR-23/MPTL-1 and predicted them to be monepantel insensitive. We challenged this hypothesis in a panel of drug tests: several species of Caenorhabditis nematodes equipped with ACR-23/MPTL-1-like receptor subunits were found susceptible to monepantel, whereas Pristionchus pacificus, closely related to these worms but lacking an ACR-23/MPTL-1 homolog, was tolerant. The parasitic nematode Strongyloides ratti, which has only a remote homolog of DES-2 and ACR-23/MPTL-1, was also tolerant to monepantel. This confirms our prediction and highlights how comparative genomic data can be used to predict a drug effect.

Porphyrin-functionalized oligo(phenyleneethynylene)s (OPE) are promising molecules for molecular electronics applications. Three such molecules (1-3) with the common structure P-OPE-AG (P and AG are a porphyrin and anchor group, respectively) and different anchor groups, viz. an acetyl protected thiol, -S-COCH3 (1), an acetyl protected thiol with methylene linker, -CH2-S-COCH3 (2), and a trimethylsilylethynyl group, -C(triple bond)C-Si(CH3)3 (3) have been synthesized and the corresponding self-assembled monolayers (SAMs) on Au(111) substrates have been prepared. The integrity and structural properties of these films were studied by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The results suggest that the films formed from 1 have a high orientational order with an almost upright orientation and dense packing of the molecular constituents, i.e. represent a high quality SAM. In contrast, molecule 2 formed disordered molecular layers on Au, even though the molecule-surface bonding (thiolate) is the same as in the case of molecule 1. This suggests that the methylene linker in molecule 2 has a strong impact on the quality of the resulting film, so that a well-ordered SAM cannot be formed. The silane system, 3, is also able to bind to the gold surface but the resulting SAM has a poor quality, being significantly disordered and/or comprised of strongly inclined molecules. The above results suggest that the nature of the anchor group along with a possible linker is an important parameter which, to a high extent, predetermines the entire quality of OPE-based molecular layers.

Centromeres in Trypanosoma cruzi and Trypanosoma brucei can be localised to regions between directional gene clusters that contain degenerate retroelements, and in the case of T. brucei, repetitive DNA., Background Trypanosomes are parasitic protozoa that diverged early from the main eukaryotic lineage. Their genomes display several unusual characteristics and, despite completion of the trypanosome genome projects, the location of centromeric DNA has not been identified. Results We report evidence on the location and nature of centromeric DNA in Trypanosoma cruzi and Trypanosoma brucei. In T. cruzi, we used telomere-associated chromosome fragmentation and found that GC-rich transcriptional 'strand-switch' domains composed predominantly of degenerate retrotranposons are a shared feature of regions that confer mitotic stability. Consistent with this, etoposide-mediated topoisomerase-II cleavage, a biochemical marker for active centromeres, is concentrated at these domains. In the 'megabase-sized' chromosomes of T. brucei, topoisomerase-II activity is also focused at single loci that encompass regions between directional gene clusters that contain transposable elements. Unlike T. cruzi, however, these loci also contain arrays of AT-rich repeats stretching over several kilobases. The sites of topoisomerase-II activity on T. brucei chromosome 1 and T. cruzi chromosome 3 are syntenic, suggesting that centromere location has been conserved for more than 200 million years. The T. brucei intermediate and minichromosomes, which lack housekeeping genes, do not exhibit site-specific accumulation of topoisomerase-II, suggesting that segregation of these atypical chromosomes might involve a centromere-independent mechanism. Conclusion The localization of centromeric DNA in trypanosomes fills a major gap in our understanding of genome organization in these important human pathogens. These data are a significant step towards identifying and functionally characterizing other determinants of centromere function and provide a framework for dissecting the mechanisms of chromosome segregation.

We present a solid polymer dye laser based on a single-mode planar waveguide. The all-polymer device is self-contained in the photodefinable polymer SU-8 and may therefore easily be placed on any substrate and be integrated with polymer-based systems. We use as the active medium for the laser the commercially available laser dye Rhodamine 6G, which is incorporated into the SU-8 polymer matrix. The single-mode slab waveguide is formed by three-step spin-coating deposition: a buffer layer of undoped SU-8, a core layer of SU-8 doped with Rhodamine, and a cladding layer of undoped SU-8.

Thermal nanoimprint lithography (NIL) of the cyclic olefin copolymeric thermoplast Topas® is demonstrated. Topas® is highly UV-transparent, has low water absorption, and is chemically resistant to hydrolysis, acids and organic polar solvents which makes it suitable for lab-on-a-chip applications. In particular, Topas® is suitable for micro systems made for optical bio-detection since waveguides for UV-light can be made directly in Topas®. In this article full process sequences for spin coating Topas® onto 4 in. silicon wafers, NIL silicon stamp fabrication with micro and nanometer sized features, and the NIL process parameters are presented. The rheological properties of Topas® are measured and the zero shear rate viscosity is found to be 2.16×104 Pa s at 170 °C and 3.6×103 Pa s at 200 °C while the dominant relaxation time is found to be 4.4 s and 0.9 s, respectively. The etch resistance of Topas® to two different reactive ion etch processes, an oxygen plasma, and an anisotropic silicon etch, is found to ...

The reaction6Li (γ, d) with Eγ around 60 MeV has been investigated with monoenergetic photons using a Si-Ge ΔE-E telescope, allowing accurate identification of deuterons with good energy resolution. A strict obedience of the isospin selection rule for E1 absorption, i.e. ΔT=1, is observed for the ground state transition.

Use of residual-state decay γ-rays could be a powerful tool in the study of photonuclear reactions. The practicality of this technique in a tagged-photon experiment is demonstrated for the first time with data on the 12C(γ,p) reaction.

The integration of optical transducers is generally considered a key issue in the further development of lab-on-a-chip microsystems. We present a technology for the integration of miniaturized, polymer based lasers, with planar waveguides, microfluidic networks and substrates such as structured silicon. The flexibility of the polymer patterning process, enables fabrication of laser light sources and other optical components such as waveguides, lenses and prisms, in the same lithographic process step on a polymer. The optically functionalised polymer layer can be overlaid on any reasonably flat substrate, such as electrically functionalised Silicon containing photodiodes. This optical and microfluidic overlay, interfaces optically with the substrate through the polymer-substrate contact plane. Two types of integrable laser source devices are demonstrated: microfluidic- and solid polymer dye lasers. Both are based on laser resonators defined solely in the polymer layer. The polymer laser sources are optically pumped with an external laser, and emits light in the chip plane, suitable for coupling into chip waveguides. Integration of the light sources with polymer waveguides, micro-fluidic networks and photodiodes embedded in a Silicon substrate is shown in a device designed for measuring the time resolved absorption of two fluids mixed on-chip. The feasibility of three types of polymers is demonstrated: SU-8, PMMA and a cyclo-olefin co-polymer (COC) -- Topas. SU-8 is a negative tone photoresist, allowing patterning with conventional UV lithography. PMMA and Topas are thermoplasts, which are patterned by nanoimprint lithography (NIL).

A review of literature related to fire evacuation in high-rise buildings was carried out with the following objectives, (1) to identify the key behavioural factors affecting the performance of people during a fire in a high-rise building, the singularities associated to this type of buildings and areas of future research; (2) to review the procedures and strategies currently adopted in high-rise buildings; (3) to review and analyse the capabilities of evacuation models by reviewing their current characteristics and applications in the context of high-rise building evacuations. The review included both findings on human behaviour in high-rise buildings and modelling techniques and tools. Different categories of building use were taken into account, namely office buildings, residential buildings and health care facilities. The individual or combined use of different egress components was analysed. Egress components include the use of stairs, elevators as well as alternative means of escape (e.g., sky-bridges, helicopters, etc.). The effectiveness of the egress components is strongly affected by the building use and the population involved. The review shows that evacuation models can be effectively employed to study relocation strategies and safety issues associated with high-rise buildings. The suitability of egress models for high-rise building evacuations is associated with their flexibility in representing different egress components and complex behavioural processes. The review highlights that there is not a definitive model to be used but that the predictive capabilities of evacuation modelling techniques would be enhanced if more than one model is employed to study different egress aspects. Future research and model developments should focus on the study of the impact of staff actions, group dynamics and people with disabilities. Given the increasing height of buildings and the gradual reduction in the physical abilities of the population, the effects of fatigue on evacuation need further studies.

Background Repeats are present in all genomes, and often have important functions. However, in large genome sequencing projects, many repetitive regions remain uncharacterized. The genome of the protozoan parasite Trypanosoma cruzi consists of more than 50% repeats. These repeats include surface molecule genes, and several other gene families. In the T. cruzi genome sequencing project, it was clear that not all copies of repetitive genes were present in the assembly, due to collapse of nearly identical repeats. However, at the time of publication of the T. cruzi genome, it was not clear to what extent this had occurred. Results We have developed a pipeline to estimate the genomic repeat content, where shotgun reads are aligned to the genomic sequence and the gene copy number is estimated using the average shotgun coverage. This method was applied to the genome of T. cruzi and copy numbers of all protein coding sequences and pseudogenes were estimated. The 22 640 results were stored in a database available online. 18% of all protein coding sequences and pseudogenes were estimated to exist in 14 or more copies in the T. cruzi CL Brener genome. The average coverage of the annotated protein coding sequences and pseudogenes indicate a total gene copy number, including allelic gene variants, of over 40 000. Conclusion Our results indicate that the number of protein coding sequences and pseudogenes in the T. cruzi genome may be twice the previous estimate. We have constructed a database of the T. cruzi gene repeat data that is available as a resource to the community. The main purpose of the database is to enable biologists interested in repeated, unfinished regions to closely examine and resolve these regions themselves using all available shotgun data, instead of having to rely on annotated consensus sequences that often are erroneous and possibly misleading. Five repetitive genes were studied in more detail, in order to illustrate how the database can be used to analyze and extract information about gene repeats with different characteristics in Trypanosoma cruzi.